Since the fabrication of graphene, designing advanced atomically thin nanomaterials (ATMs) with few-atoms thick layers, special electronic structures, and excellent electrochemical properties for next-generation energy storage and conversion devices has attracted worldwide attention. Compared with traditional bulk materials, the ATMs exhibit several advantages: i) Their large specific surface area offers abundant active sites for ion insertion/deinsertion, and increases the contact with the electrolyte; ii) The atomic thickness of ATMs conspicuously shortens the ion diffusion pathway; iii) The distorted crystal lattice of ATMs could lead to increased electrical conductivity, and also facilitate vacancy generation, elemental doping and heterostructure construction; iv) The ATMs are regarded as an ideal 2D platform to explore the connection between electrochemical performance and electronic structures. However, they also face challenges like weak conductivity, large bandgap, and poor chemical activity. To solve these problems, various methods, including doping/phase engineering, vacancies/hole creation, and heterostructure construction have been utilized to optimize their properties. The goal of this thesis is to present a deep understanding of the impact of structural design and engineered defects on the electrochemical performance of ATMs. In the first study, holey graphene (HG) was created through an etching method, which acted as a template for the in-situ growth of atomically thin mesoporous NiCo2O4 nanosheets, leading to a NiCo2O4-HG heterostructure. The atomic-thin thickness and porous structures of NiCo2O4-HG was beneficial for electrolyte diffusion and ions/electrons transfer, and the subsequent numerous accessible surface atoms result in improved redox pseudocapacitance. In addition, the synergistic effect between NiCo2O4 and HG produced a broad interfacial area and increased electrical conductivity, dramatically accelerating the intercalation pseudocapacitance. Both redox and intercalation pseudocapacitive energy storage are beneficial for achieving high energy and power density in lithium-ion batteries (LIBs). Consequently, the NiCo2O4@HG delivered a high specific capacity of 1103.4 mAh g-1 at 0.2 C, ~88.9% contribution from pseudocapacitance at 1 mV s-1 and ultra-long life up to 450 cycles with 931.2 mAh g-1 retention, significantly outperforming previously reported electrodes. Vacancies engineering is an effective way to optimize the properties of ATMs. However, cation vacancies have rarely been reported for batteries because of the challenging creation process. Thus, we applied an alkaline etching strategy to produce Co vacancies (VCo) at the interface of ultra-thin Co3-xO4/graphene@CNT for highenergy/ power LIBs. The existence of VCo were confirmed by HRSTEM, XPS, and ELLS. The Co3-xO4/graphene@CNT showed a high capacity of 1688.2 mAh g-1 at 0.2 C, outstanding rate capability of 83.7% capacity retention at 1 C, excellent cycling performance (1500 cycles with a reversible capacity of 1066.3 mAh g-1), and a large pseudocapacitive contribution (86.5%) induced by VCo at the interface of Co3-xO4/graphene@CNT. Density functional theory (DFT) indicates that the VCo could significantly improve Li adsorption and provide more pathways with a lower energy barrier for Li diffusion, leading to obvious intercalation pseudocapacitive behavior and high-capacity/rate energy storage. Inspired by the effect of VCo on the battery performance of Co3-xO4/graphene@CNT, we also created VCo on the interface of Co1-xSe2/graphene (Co1-xSe2/GE) which was utilized as anode for SIBs. The DFT result indicated that due to the VCo the Co1-xSe2/GE exhibited higher sodium adsorption energy (4.57 eV) and lower sodium diffusion barrier (~1.7 eV) which is beneficial for the intercalation and diffusion of Na+. Experimental results confirmed that the tuned electronic state of Co in Co1-xSe2/GE could result in high specific capacity (626.2 mAh g-1 at 0.2 C), outstanding rate capacity, large pseudocapacitive contribution ratio and an exceptional cycling performance superior to most CoSe2-based anodes. The outstanding energy storage performance of Co1-xSe2/GE may be due to the synergistic effect between ultrathin CoSe2 nanobelts and GE nanosheets, which could provide multiple diffusion pathways, added active sites, and lower Na+ diffusion barriers leading to excellent pseudocapacitance behaviour. This work implied that VCo could stimulate the potential of CoSe2 to facilitate the development of low-cost energy storage devices. In addition to application in batteries, we also explored the potential of ATMs for the oxygen evolution reaction (OER). In the final work, we focused on the role of S on the OER activity of ultrathin FeCoOOH and used DFT to confirm the catalytically active centres. The results suggest the electronic states of Co could be optimized by the synergistic effect between two coordinating S and one adjacent Fe, leading to decreased binding energy of OH* (ΔEOH) while rarely changing ΔEO, thereby dramatically lowering the overpotential of the catalytic activity. Further experimental studies verified the synergistic effect between S and Fe on tuning the electronic structure of Co(OH)2, which greatly improved its catalytic activity with a small overpotential of 225.3 mV to drive to a current density of 20 mA cm-2. This work unveils the origin of the high catalytic activity of transition metal sulfides in the atomic level and provides insights into the prospect of ATMs as efficient OER electrocatalysts. In summary, the research exhibited in this thesis indicated that defect engineering of ATMs could increase the surface active sites, provide an additional pathway for ions/electrons transfer, and increase the pseudocapacitance contribution resulting in outstanding battery performance. ATMs also showed impressive potential for electrocatalysis application. These bottom-up synthesis methods and defect engineering were also validated for other transition metal oxides/ dichalcogenides for different energy storage and conversion devices.