Manganese sulfide (MnS), a member of transition metal sulfides, has been considered as a promising anode material for reversible Li storage due to its high theoretical capacity and structural advantages. However, the intrinsic electrochemical performance of MnS with different phases in lithium-ion batteries is yet to be fully investigated. Herein, high purity rock-salt (RS), zinc-blende (ZB) and wurtzite (WZ) MnS nanocrystals with different morphologies were successfully synthesized via a facile solvothermal method. The RS-MnS, ZB-MnS and WZ-MnS electrodes showed the capacities of 232.5 mAh g−1, 287.9 mAh g−1 and 79.8 mAh g−1 at the 600th cycle, respectively. ZB-MnS displayed the best performance in terms of specific capacity and cyclability in comparison to RS-MnS and WZ-MnS nanocrystals. Interestingly, all the three kinds of MnS electrodes exhibited an unusual phenomenon of capacity increase upon cycling along with reduced particle sizes and without change in crystallinity. The main contribution of capacity increase was ascribed to the decreased cell resistance and enhanced interfacial charge storage, which facilitated more effective Li+ diffusion into electrode materials.