As one of the most promising negative electrode materials in lithium-ion batteries (LIBs), SnO2 experiences intense investigation due to its high specific capacity and energy density, relative to conventional graphite anodes. In this study, for the first time, atomic layer deposition (ALD) is used to deposit SnO2, containing both amorphous and crystalline phases, onto graphene nanosheets (GNS) as anodes for LIBs. The resultant SnO2-graphene nanocomposites exhibit a sandwich structure, and, when cycled against a lithium counter electrode, demonstrate a promising electrochemical performance. It is demonstrated that the introduction of GNS into the nanocomposites is beneficial for the anodes by increasing their electrical conductivity and releasing strain energy: thus, the nanocomposite electrode materials maintain a high electrical conductivity and flexibility. It is found that the amorphous SnO2-GNS is more effective than the crystalline SnO2-GNS in overcoming electrochemical and mechanical degradation; this observation is consistent with the intrinsically isotropic nature of the amorphous SnO2, which can mitigate the large volume changes associated with charge/discharge processes. It is observed that after 150 charge/discharge cycles, 793 mA h g−1 is achieved. Moreover, a higher coulombic efficiency is obtained for the amorphous SnO2-GNS composite anode. This study provides an approach to fabricate novel anode materials and clarifies the influence of SnO2 phases on the electrochemical performance of LIBs.