Rapid progress of lithium‐ion batteries (LIBs) highly relies on high‐performance electrode materials. Herein, a novel nanocomposite of CoSn alloy with a multishell layer structure confined in 3D porous carbon is constructed through a facile freeze drying and annealing treatment method. The skillful design effectively relieves the volume expansion of the Sn‐based alloy and enhances the combination between CoSn and carbon. Profiting from the synergistic effect of the multibuffer structure alloy and cross‐linked porous carbon, CoSn@SnOx/CoOx@C displays high capacity (912.6 mA h g−1 after 100 cycles at 0.1 A g−1) and excellent cycling stability (almost no capacity decay at 10 A g−1 after 1000 cycles) when used as anode for LIBs. The presence of Sn–O/Co–O bond makes the nanoalloy tightly pinned on the carbon substance and the structure stability of electrode material is improved significantly. Furthermore, the porous carbon with plentiful defects offers abundant room for the volume expansion of Sn and ensures fast transport of electrons/ions. Cyclic voltammogram (CV) curves under different scan rates reveal that the charge storage of the nanocomposite is controlled by pseudocapacitive and ion‐diffusion mechanisms. This facile fabrication strategy and unique structure design can be extended to other composite materials for energy storage devices.