The rational design of the catalysts with easily-accessible surface and high intrinsic activity is desirable for electrocatalytic hydrogen evolution reaction (HER). Here, we reported the construction of two-dimensional (2D) Co-Mo nitrides based heterojunctional catalyst for efficient HER based on a “mediated molecular” assisted route. The 2D Co(OH)2 sheet reacted partially with the “mediated molecular” (2-methylimidazole (2-MIM)) to form zeolitic imidazolate framework (ZIF)-67 at surface, giving ZIF-67/Co(OH)2 sheets. The ZIF-67 combines with [PMo12O40]3− cluster (PMo12) due to the interaction of mediated molecular with PMo12, producing 2D Mo-Co-2MIM/Co(OH)2 bimetallic precursor. After controlled nitriding, the Mo2N islands dispersed on 2D porous Co-based sheets were formed. A series of characterizations and density functional theory (DFT) calculation indicated the formation of a close contact interface, which promotes the electron transfer between Mo and Co components, enhances the electron migration/redistribution and redistribution and down-shift of d-band center and thus gives a high intrinsic activity. The 2D characteristics make the catalyst more accessible contact sites, which is favourable to promot the HER. The tests showed that the optimized catalyst exhibits an onset potential of 0 mV and an overpotential of 10 mA·cm−2 at 35.0 mV, which is quite close to that of Pt/C catalyst. It also exhibits an activity superior to Pt/C at high current density (> 100 mA·cm−2). A good stability of the catalyst was achieved with no significant decay for 100 h of continuous operation. The electrolytic cell composed of optimized catalyst and P-NiFe-layered double hydroxide (LDH) can be driven by low voltage (only 1.47 V) to reach a current density of 10 mA·cm−2.