Optimizing the electronic configuration of Mo2C by activating heteroatom(s)-neighboring carbon atoms to enhance the activity of hydrogen evolution reaction (HER) has been demonstrated. However, the development of heteroatom-doped Mo2C to fabricate a water electrolyzer is still a challenge because of the limitation of a well-defined electronic structure of hybridization of Mo with heteroatom(s). Here, nitrogen (N) and phosphor (P) codoped Mo2C embedded carbon nanotubes (NCNT@P,N-Mo2C) with the priority occupation of C-sites by N, which well confines the P-implantation at the pyrrodic N-sites and brings out N-O bonding on the surface, which favorably modifies the electronic configuration of adjacent Mo, resulting in highly efficient pH-tolerant HER activity. This study not only presents a potential HER electrocatalyst candidate but also provides a strategy for the construction of a well-defined electronic structure of heteroatom(s)-neighboring carbon-based materials.