Surface coating has become an effective method to stabilize solid-electrolyte interphase (SEI), extend the cycle life, and improve rate performance of anode materials for lithium ion batteries (LIBs). However, owing to the incompatible volumetric changes between the core and the shell, core-shell structures with fully filled active materials are prone to fracture upon electrochemical cycling, leading to fast capacity fading. Here, we synthesize partially filled Sn@C yolk-shell nanoparticles (NPs) by chemical vapor deposition (CVD) as anode materials for LIBs. Our in situ transmission electron microscope (TEM) studies demonstrate that the yolk-shell NPs can lithiate and delithiate hundreds of cycles with ultrafast (2s per cycle) reversible cycling without rupture. Front-tracking finite element analysis of the coupled chemical reaction, diffusion, and stress generation upon lithiation reveals improved chemomechanical durability of the yolk-shell NPs, in comparison to naked SnNPs and fully filled Sn@C core-shell NPs. Our results provide rational guidance to the development and optimization of yolk-shell NPs as high-performance anode materials for LIBs.