Two-phase heterostructure with rich phase boundaries holds great potential in engineering advanced electrode materials. However, current heterostructures are largely generated by introducing exotic cations or anions, complicating synthetic procedures and disturbing real insights into the intrinsic effect of heterostructure. Herein, nanosized monometallic selenides heterostructures are developed by precisely controlled selenylation of metal organic frameworks, which are implanted into in-situ formed carbon (NiSe/NiSe2@C, CoSe/CoSe2@C). The disordered atoms arrangement at two-phase boundary leads to the redistribution of interfacial charge and generation of lattice distortions, promoting easy adsorption and swift transfer of Li+, and providing extra active sites. As a proof of concept, the NiSe/NiSe2@C exhibits far surpassing lithium storage properties to single-phase counterparts (NiSe@C and NiSe2@C), including higher reversible capacity of 1015.5 mAh g− 1, better rate capability (500.8 mAh g− 1 at 4 A g− 1), and superior cyclic performance. As expected, the NiSe/NiSe2@C manifests lower charge transfer resistance, higher Li+ diffusion coefficient, and accelerated capacitive kinetics. Ex-situ X-ray diffraction, high-resolution transmission electron microscopy, and selected area electron diffraction combined with differential capacity versus voltage plots reveal multi-step redox mechanism of NiSe/NiSe2@C and the reason of conspicuous capacity enhancement. This work demonstrates the enormous potential of monometallic monoanionic heterostructure in energy-related field.