The introduction of heteroatoms is one of the most important ways to modulate the intrinsic electronic structure of electrocatalysts to improve their catalytic activity. However, for transition metal chalcogenides with highly symmetric crystal structure (HS-TMC), the introduction of heteroatoms, especially those with large atomic radius, often induces large lattice distortion and vacancy defects, which may lead to structural phase transition of doped materials or structural phase reconstruction during the catalytic reaction. Such unpredictable situations will make it difficult to explore the connection between the intrinsic electronic structure of doped catalysts and catalytic activity. Herein, taking thermodynamically stable cubic CoSe2 phase as an example, we demonstrate that nitrogen incorporation can effectively regulate the intrinsic electronic structure of HS-TMC with structural phase stability and thus promote its electrocatalytic activity for the hydrogen evolution activity (HER). In contrast, the introduction of phosphorus can lead to structural phase transition from cubic CoSe2 to orthorhombic phase, and the structural phase of phosphorus-doped CoSe2 is unstable for HER.