Mostly reported MoSe2 suffered from easily stacking problem, volume expansion and relative low capacity. From the experience of Li/Na-Se batteries, the exfoliated and encapsulated MoSe2 inside carbon nanospheres with C-O-Mo bonds and large layer distance (0.89 nm) are successfully constructed. This unique effective structure has C-O-Mo bonding allowing high conductivity across the Se-O insulation layer and promoting its reversible conversion. The first-principles calculations demonstrated that the frontier molecular orbitals of C-O-Mo interface structure are mainly localized on the MoSe2 sheet fragment with an appropriate HOMO-LUMO gap (< 4eV),suggesting its good stability and conductivity. Utilized as anodes for LIBs allows a Li-storage capacity to be realized of 1208 mAh g -1 after 150 cycles at 1.0 A g -1 and 519 mAh g -1 after 200 cycles at 4.0 A g -1 . The Na-storage capacity is found to be 543, 491 mAh g -1 after 120 cycles at 0.1, 1.0 A g -1 . Focusing on the analysis of CV, the reducing particle may improve the capacitive behaviors, further resulting the high-rate performance. Ex-situ techniques demonstrated that the emerging Se was constrained uniformly. The controlling of by-product Se plays a key role in achieving a high rate 2 capacity and cycling stability, and opens up a potential avenue for these metal-selenide anodes designs for battery storage systems.