Sn anode in rechargeable lithium ion batteries (LIBs) is currently being intensely investigated due to high reversible capacity and energy density as compared to the commercialized graphite anode. However, large volume change upon cycling causes poor cyclic performance, which prevents the practical application of Sn anode in LIBs. In this study, the nanosized M x Sn (M=Ni, Fe, and Cr) alloys were encapsulated in amorphous carbon nanotubes (ACNTs) creating hybrid anode heterostructures. The structure of the hybrid anodes was confirmed by X-ray diffraction (XRD), field emission scanning electron microscope (FE-SEM) and high angle dark field scanning transmission electron microscope (HAADF-STEM), and demonstrated that Ni3Sn4, FeSn2, and Cr2Sn3 alloys exist in the hybrid anodes as both nanowires and nanoparticles. The galvanostatic cycling originating from over 330 charge–discharge cycles indicated that encapsulation of Ni3Sn4, FeSn2, and Cr2Sn3 into ACNTs results in surprisingly excellent cycling performance, high rate capability, and increased initial coulombic efficiency (81.4%). Ex situ HAADF-STEM images of anodes after cycles showed that one-dimensional ACNTs as well as electrochemically inactive phase M (Ni, Fe, and Cr) in M x Sn function as good matrices, offering “buffer zone” to effectively accommodate the mechanical stress induced by Sn anode expansion and shrinkage. Importantly, ACNTs enable electrical contact of Sn nanoparticles with the current collectors. Therefore, our design can significantly overcome electrochemical degradation of anodes with large volume change, resulting in increased LIB performance.