MoS2 is a promising anode material in sodium-ion battery technologies for possessing high theoretical capacity. However, the sluggish Na+ diffusion kinetics and low electronic conductivity hinder the promises. Herein, a unique MoS2/FeS2/C heterojunction with abundant defects and hollow structure (MFCHHS) was constructed. The synergy of defect engineering in MoS2, FeS2, and the carbon layer of MFCHHS with a larger specific surface area provides multiple storage sites of Na+ corresponding to the surface-controlled process. The MoS2/FeS2/C heterostructure and rich defects in MoS2 and carbon layer lower the Na+ diffusion energy barrier. Additionally, the construction of MoS2/FeS2 heterojunction promotes electron transfer at the interface, accompanying with excellent conductivity of the carbon layer to facilitate reversible electrochemical reactions. The abundant defects and mismatches at the interface of MoS2/FeS2 and MoS2/C heterojunctions could relieve lattice stress and volume change sequentially. As a result, the MFCHHS anode exhibits the high capacity of 613.1 mA h g−1 at 0.5 A g−1 and 306.1 mA h g−1 at 20 A g−1. The capacity retention of 85.0% after 1400 cycles at 5.0 A g−1 is achieved. The density functional theory (DFT) calculation and in situ transmission electron microscope (TEM), Raman, ex-situ X-ray photon spectroscopy (XPS) studies confirm the low volume change during intercalation/deintercalation process and the efficient Na+ storage in the layered structure of MoS2 and carbon layer, as well as the defects and heterostructures in MFCHHS. We believe this work could provide an inspiration for constructing heterojunction with abundant defects to foster fast electron and Na+ diffusion kinetics, resulting in excellent rate capability and cycling stability.