N-doped hollow carbon nanospheres (NHCS) with mesoporous carbon shells is selected as nanoreactors and encapsulated with few-layered MoS2 nanosheets to monitor its electrochemical properties and structural conversion in long-term cycling. Mesoporous walls of NHCS can facilitate electrolyte penetration and provide conductive shells for superior mass diffusion and charge transfer. When serving as SIB anodes, MoS2@NHCS has a capacity value of 371 mAh g-1 at 1 A g-1 with a capacity retention of 94.9% after 100 cycles which is higher than powder form MoS2 and is among the highest values of earlier reported MoS2 electrodes. The origin of gradual capacity decay of MoS2@NHCS anodes in-between 50 to 150 cycles has been investigated. Transmission electron microscopy and ex-situ X-ray diffraction have shown significant morphology change of space-confined MoS2 and the production of MoO3 together with oxygen-deficient MoOx after continuous charge/discharge test. After long-term cycle test of MoS2@NHCS, the ratios of Mo6+ and Mo5+ increased significantly with the decreasing of Mo4+ ratio, while the sulfur from MoS2 transformed from S2− to SO4 2−. This work highlight the phase transformation and composition change of MoS2 for MoS2-based anode in long-duration charge/discharge tests.