To understand the effect of a polydopamine interlayer between a copper current collector and a silicon composite electrode, a physics‐based model is used to analyze the cycle performance of silicon‐based lithium‐ion half‐cells with bare and polydopamine‐treated copper current collectors. We investigate the capacity‐fading mechanisms of the two cell configurations by analyzing the model parameters that change with cycling. The major capacity‐fading mechanisms in the silicon‐based anodes are the increase in film resistance (solid electrolyte interphase resistance and contact resistance) and the isolation of silicon active material. The polydopamine interlayer reduced the contribution of the film resistance and isolation of the silicon active material to the capacity fade by 22 % and 10 %, respectively. The insulating‐nature of the polydopamine interlayer resulted in an increase in the charge transfer resistance contributing to 15 % reduction in the capacity retention. The efficacy of the physics‐based model is validated with experimental data obtained from silicon‐based half‐cells with bare and polydopamine‐treated copper current collectors.