Molybdenum disulfide (MoS₂) holds great promise as an advanced anode material for lithium ion batteries, but suffers from poor electrochemical performance, especially cycling stability. Here, we report micron-sized particulates composed of encapsulated-type MoS₂/C hybrid nanostructures which provide an effective confinement effect to soluble intermediate products during cycling reactions, offering a physically robust framework and locally stable sites for MoS₂-based electrode reactions during the cycling process. The micron-sized MoS₂/C exhibits a high specific capacity of 1343 mA h g⁻¹ on average at 0.1 A g⁻¹, excellent rate performance (929 mA h g⁻¹ at 1 A g⁻¹), and remarkable cycling stability with 1250 mA h g⁻¹ retention at 1 A g⁻¹ after 480 cycles. In addition, we further clarify the uniform redistribution of S and Mo in the carbon matrix during the decomposition of MoS₂ nanoparticles which demonstrates the confinement effect of hybrid structures thus leading to an enhanced electrochemical performance, providing a meaningful suggestion for the rational design of sulfide- and selenide-based carbon hybrid electrodes for practical applications.