Electrocatalytic overall water splitting technology has received considerable attention in recent years. The fabrication of low-cost, earth-rich and potent bifunctional electrocatalysts is vital for hydrogen evolution (HER) and oxygen evolution reactions (OER). Herein, the N and S co-doped NiCo2O4@CoMoO4 heterostructures (N, S–NCO@CMO400) are fabricated by CVD and hydrothermal methods. N and S atoms as auxiliary active centers can increase the activity of Ni, Co and Mo atoms at the same time. Hierarchical heterostructures generate more interfaces to accelerate mass transfer and enlarge the electrochemical surface area, which greatly enhances the catalytic activity. The catalyst displays outstanding OER performance. The overpotentials of OER and HER are 165 and 100 mV at a current density of 10 mA cm−2, respectively. More importantly, the N, S–NCO@CMO400-based water splitting cell has a low voltage of 1.46 V at 10 mA cm−2. Furthermore, the N, S–NCO@CMO400 runs for 120 h in stable operation. This work provides new ideas for the design of hierarchical heterostructures with two-element incorporation.