We develop a novel method combining co-precipitation and post thermal treatment to synthesize Sn-MnO@N-doped carbon yolk-shelled three-dimensional (3D) interconnected networks. In the novel nanostructures, Sn-MnO nanoparticles are wrapped by N-doped amorphous C with 3D interconnected networks to compensate the volume expansion of active substances during Li+ insertion. Owing to the prominent merits of these structural features, Sn-MnO@N-doped carbon composites exhibit high special capacity (1185.9 mAhg(-1)) and excellent cyclic stability (757.2 mAhg(-1) at 0.1 Ag-1 after 200 cycles). Even after 500 cycles, a capacity of 535.8 mAhg(-1) at 0.5 Ag-1 can still be maintained. The investigation confirms that the improved performances of the composite can be attributed to the synergistic effects of N-doped carbon coating yolk-shelled 3D interconnected networks, nano-sized Sn-MnO cores and the in-depth nanocrystallization process during intense cycles. This unique structure design of carbon coating Sn-based nanoparticles yolk-shelled 3D interconnected networks can be applied to other anode nanomaterials in lithium-ion batteries.