Quantifying the irreversible chemical and structural changes of Si during cycling remains challenging. In this study, a continuous reactive molecular dynamics delithiation algorithm, with well-controlled potential gradient and delithiation rate, was developed and used to investigate the "natural" delithiation responses of an aluminum-oxide coated silicon thin-film. Fast delithiation led to the formation of dense Si network near the surface and nanoporosity inside the a-LixSi, resulting in 141% volume dilation and significant amount of Li trapped inside (a-Li1.2Si) at the end of delithiation process. In contrast, slow delithiation allowed the a-LixSi to shrink by near-equilibrium condition, demonstrating no permanent inner pore with nearly Li-free structure (a-Li0.2Si) and minimal volume dilation (44%). However, even without trapped Li, the delithiated a-LixSi still exhibited higher volume (lower density) than the equilibrium structure with the same Li concentration, despite delithiation rate. The origin of this excess volume is the loss of directly bonded Si–Si pairs, which made the subsequent relithiation faster. On the basis of the atomistic modeling and the quantified degradation mechanism, battery operating guidelines, including the delithiation rate and the depth of charge to avoid trapped Li and coating delamination, were suggested to improve the durability Si electrodes. [ABSTRACT FROM AUTHOR]