Heterostructure engineering holds exceptional promise for the development of high-performance electrocatalysts for overall water splitting. However, production of inexpensive and high-efficiency bifunctional electrocatalysts remains a challenge. Herein, we demonstrate a simple method to synthesize a paper-mulberry (Broussonetia papyrifera)-in-spired Co9S8@CoNi2S4/nickel foam (Co9S8@CoNi2S4/NF) heterojunction with high catalytic activity and stability. The process involves in situ growth of NiCo layered double hydroxide and in situ derivatization of ZIF-67, followed by the S heteroatom doping. The Co9S8@CoNi2S4/NF benefits from the heterostructure and functional advantages of multidimensional building blocks including one-dimensional (1D) nanowires, 2D nanosheets and nanoparticles. The optimized Co9S8@CoNi2S4/NF heterojunction with 10% sulphur content reveals excellent electrocatalytic activity with the lower over-potentials of 68 mV for hydrogen evolution reaction (HER) and 170 mV for oxygen evolution reaction (OER) at 10 mA cm−2 in the 1.0 mol L−1 KOH solution, which is superior to the recently reported transition metal based electrocatalysts. The outstanding performance is attributed to the strong interface coupling between CoNi2S4 and Co9S8, the advantage of multidimensional structure and the customized electronic structure. The density functional theory suggests that the interface between Co9S8 and CoNi2S4 optimizes the adsorption of the multiple intermediates and further facilitates water splitting kinetics. This work offers a generic approach for heterostructure engineering design of high-performance catalytic system applications.