The exploring of economical, high‐efficiency, and stable bifunctional catalysts for hydrogen evolution and oxygen evolution reactions (HER/OER) is highly imperative for the development of electrolytic water. Herein, a 3D cross‐linked carbon nanotube supported oxygen vacancy (Vo)‐rich N‐NiMoO4/Ni heterostructure bifunctional water splitting catalyst (N‐NiMoO4/Ni/CNTs) is synthesized by hydrothermal‐H2 calcination method. Physical characterization confirms that Vo‐rich N‐NiMoO4/Ni nanoparticles with an average size of ≈19 nm are secondary aggregated on CNTs that form a hierarchical porous structure. The formation of Ni and NiMoO4 heterojunctions modify the electronic structure of N‐NiMoO4/Ni/CNTs. Benefiting from these properties, N‐NiMoO4/Ni/CNTs drives an impressive HER overpotential of only 46 mV and OER overpotential of 330 mV at 10 mA cm−2, which also shows exceptional cycling stability, respectively. Furthermore, the as‐assembled N‐NiMoO4/Ni/CNTs||N‐NiMoO4/Ni/CNTs electrolyzer reaches a cell voltage of 1.64 V at 10 mA cm−2 in alkaline solution. Operando Raman analysis reveals that surface reconstruction is essential for the improved catalytic activity. Density functional theory (DFT) calculations further demonstrate that the enhanced HER/OER performance should be attributed to the synergistic effect of Vo and heteostructure that improve the conductivity of N‐NiMoO4/Ni/CNTs and facilitatethe desorption of reaction intermediates. By a simple hydrothermal‐H2 calcination method, the secondary aggregated metal nanoparticles with heterojunctions and abundant oxygen vacancies are loaded on carbon nanotubes (N‐NiMoO4/Ni/CNTs). Operando Raman results reveal that Ni2+‐OH* and C‐H* as the active sites of HER process, γ‐NiOOH serves as the active intermediates of OER process for N‐NiMoO4/Ni/CNTs.