Hollow nano-/micromaterials with tunable shell architectures and compositions are becoming increasingly important and attractive for electrochemical energy conversion and storage. Here, we report carbon-incorporated mixed anionic nickel phosphorus-selenium (Ni0.85Se|P) hollow yolk-shell microspheres synthesized by simultaneous selenization and phosphatization of Ni-based metal organic framework (Ni-MOF). Our experimental results indicated that P-doping reduces the synthesis temperature of the system and enhances the crystallinity of Ni0.85Se. As a result, this unique structure (Ni0.85Se|P) with better crystallinity and higher Ni2+/Ni3+ ratio shows outstanding specific capacity of 506 C g−1 at 1 A g−1. And the assembled Ni0.85Se|P//AC hybrid supercapacitor shows high power density of 20.7 Wh kg−1 at energy density of 798.7 W kg−1. Meanwhile, Ni0.85Se|P exhibits smaller Tafel slope of 90 mV dec−1 and lower onset overpotential of 179 mV versus reversible hydrogen electrode (RHE) for hydrogen evolution reaction (HER) than that of NiP2 and Ni0.85Se, which demonstrates the modulated electronic structure of Ni0.85Se|P. Our study will provide a new strategy for combining P-doped induced high crystallinity mixed anion transition metal complexes with MOF of hollow structures for energy storage device and HER.