Constructing Mott–Schottky heterojunctions in nanohybrids is an effective strategy for facilitating electron transfer and optimizing the electronic structure of active sites; however, challenges remain. Herein, a selenium‐induced phase separation strategy is proposed and successfully construct NiSe2/MoSe2 Mott–Schottky heterojunctions on N‐doped brain coral carbon nanospheres (N‐BCCSs). Owing to built‐in electric fields, optimized electronic density, and unique nanoflake/sphere structures, the designed NiSe2/MoSe2@N‐BCCSs carbon‐based Mott–Schottky catalysts achieved satisfactory electrocatalytic performance. When serving as a counter electrode for the triiodide reduction reaction (IRR), a power conversion efficiency of 8.49% is obtained, which outperformed that of conventional Pt electrodes (7.80%). When the NiSe2/MoSe2@N‐BCCSs are used as electrocatalysts for the hydrogen evolution reaction (HER), their overpotential (η10) is as low as 119 mV, which is significantly better than that of other transition‐metal selenides. This research demonstrates a new concept for constructing Mott–Schottky heterojunctions and provides a new direction for investigating multifunctional carbon‐based composites.