Heavy metal contamination has been demonstrated to possess the severe threats toward the whole ecosystems and public security even at trace levels. Therefore, it is essential to exploit an ultrasensitive technique to determine the levels of heavy metal ions. In this work, hierarchical MgFe-layered double hydroxide (MgFe-LDH) microspheres have been successfully immobilized on the graphene nanosheets surface via a facile one-step hydrothermal route. Benefiting from the synergistic effects associated with high specific surface area, strong affinity of hierarchical MgFe-LDH architecture toward heavy metal ions, good electrical conductivity and effective electron transfer efficiency of graphene, the resulting composite (denoted as MgFe-LDH/graphene) is explored as an electrochemical sensor for simultaneous detection of Pb(II) and Cd(II) in aqueous medium. As a consequence, MgFe-LDH/graphene modified electrode exhibits low detection limit of 5.9 nM for Cd(II) and 2.7 nM for Pb(II), which are dramatically lower than the respective values of 3 ppb (27 nM) and 10 ppb (48 nM) in domestic water permitted by the World Health Organization (WHO). Meaningfully, the proposed electrochemical sensor shows specific recognition capability to Pb(II) and Cd(II), excellent reproducibility in repetitive measurements as well as feasibility in real water analysis.