The degradation of lithium-ion batteries (LIBs) is caused by a complicated mechanism; therefore, identifying their degradation mechanism remains challenging. Most studies related to the degradation mechanism of LIBs have focused on the degradation of cathode and anode materials. A separator that provides a pathway for Li+ ions is crucial for good electrochemical performance and safety of LIBs, but its degradation mechanism has rarely been studied. This study analyzed the relationship between the structural deformation of an aged separator and the electrochemical performance of LIBs. We discovered that even if the polyethylene (PE) separator is exposed to prolonged cycling under normal charging and discharging conditions, the by-products formed via electrolyte decomposition are firmly trapped in its pore, resulting in pore clogging. Additionally, the PE polymer chain gradually oxidizes at the part that is in contact with the cathode side, resulting in the loss of elasticity and breaking the polymer chain in the PE separator. These degradation processes of the PE separator can cause poor Li+ ion conductivity throughout the aged separator, which eventually results in lower electrochemical performance, particularly the rate performance, of LIBs.