Tin-based metal oxides usually suffer from severe capacity fading resulting from aggregation and considerable volume variation during the charge/discharge process in lithium ion batteries. In this work, a novel nanocomposite (MTO/N-RGO) of hollow amorphous MnSnO3 (MTO) nanoparticles and nitrogen-doped reduced graphene oxide (N-RGO) has been designed and synthesized by a two-step method. Firstly, the nitrogen-doped graphene nanocomposite (MTO/N-RGO-P) with MnSn(OH)6 crystal nanoparticles was synthesized by a facile solvothermal method. Subsequently, the MTO/N-RGO nanocomposite was obtained through the post heat treatment of MTO/N-RGO-P. The designed heterostructure and well-combination of the hollow amorphous MTO and N-RGO matrix can accelerate the ionic and electronic transport, and simultaneously accommodate the aggregation and volume variation of MTO nanoparticles during the lithiation–delithiation cycles. The as-prepared hybrid of MTO and N-RGO (MTO/N-RGO) exhibits a high reversible capacity of 707mAhg−1 after 110 cycles at 200mAg−1, superior rate capability, and long-term cyclic life with high capacity of 610mAhg−1 over 1000 cycles at 400mAg−1. Superior capacity retention of 97.3% over 1000 cycles was obtained. This work opens new opportunities to fabricate the high-performance electrode materials with heterostructure for lithium storage systems, especially for novel multi-metal oxide based nanocomposites with high cycling stability.