Heterostructure electrocatalysts have garnered widespread attention for effectively enhancing electrocatalytic activity. However, less attention has been paid to ternary nitride heterostructure catalysts for the hydrogen evolution reaction (HER), and their synthesis remains challenging. In this study, a Co3Mo3N/Ni3Mo3N heterostructure catalyst on nickel foam (NF) is designed and prepared via high-temperature nitridation of the heterostructured precursor. The resulting 1D/3D hierarchical structure electrode, featuring rich heterointerfaces, provides abundant active sites, enhancing mass transport and charge transfer. Experimental results reveal strong electronic interactions at the heterointerface, while density functional theory (DFT) calculations establish that Co3Mo3N/Ni3Mo3N possesses a lower water dissociation energy barrier and optimized hydrogen adsorption energy. Consequently, it demonstrates excellent HER performance, exhibiting low overpotentials of 36 mV in alkaline and 58 mV in neutral media at 10 mA cm−2. This study presents an innovative approach to designing ternary nitride heterostructure catalysts with enhanced HER activity, applicable to other heterostructure catalysts.