As a new type of negative electrode material, tin-based material exhibits a high theoretical capacity. However, tin-based anode materials always undergo severe volume change upon alloying reaction during lithium insertion and extraction, which leads to the pulverization of the active materials and poor electrochemical performance, seriously hampering its practical application. In this work, oxygen-containing group functionalized carbon nanotubes (FCNTs) were facilely obtained, and the three-dimensional crosslinked SnSe2-SnO2@FCNTs multiphase materials were prepared by solvothermal and high-temperature heat treatment. The formation of Sn-O-C bonds from oxygen-containing functional groups of FCNTs combined with Sn can promote the electric connection and integrity of the composites. The implanted defects in FCNTs can not only be beneficial to anchoring SnO2 and SnSe2 nanoparticles, but also helpful to the penetration of Li+ ions into the electrodes from electrolyte. In addition, the large Fermi energy difference between SnSe2 and SnO2 nanoparticles results in the formation of a built-in electric field at the interface of the multiphase materials, accelerating the diffusion of ions. The smaller size of the multiphase materials leads to significant pseudocapacitive behavior, which facilitates the highly reversible surface/interface adsorption. Under the multiple effects of FCNTs, SnSe2, and SnO2, the SnSe2-SnO2@FCNTs multiphase materials exhibited excellent electrochemical performance. At a current density of 0.1A·g-1, a discharge specific capacity of 898.0mAh·g-1 was achieved. When the current density was increased to 2A·g-1, it still exhibited a discharge specific capacity of 443.9mAh·g-1. After a long charge/discharge cycling at 1A·g-1 over 450 cycles, it still showed a specific capacity of ~ 400mAh·g-1. This work significantly demonstrated the enhanced Li-storage performance of SnSe2-SnO2 heterostructures incorporated in the functionalized multi-walled CNTs. This opens a new way to synthesize advanced tin-based materials as high-performance anodes for high-energy density lithium-ion batteries.