Abstract Most separators for lithium‐ion (Li‐ion) batteries are manufactured using polyolefins. However, such thermoplastic materials may undergo structural changes under high voltage or temperature. Thus, this study investigates the structural and morphological changes of separators during overcharge conditions. Unlike a single‐layer polypropylene (PP) separator, a composite separator with an interface, such as a PP/polyethylene (PE)/PP separator, exhibits a characteristic peak in voltage during the overcharging process before the occurrence of the shutdown mechanism by the PE layer. As the temperature rises, parts of the irregular crystalline structure of PE melt because of their lower melting temperature at the PP/PE interface. This results in local shrinkage and interfaces disturbance, and the Li‐ion channel becomes partially blocked. The Li‐ions follow alternative channels, and this causes the voltage to abruptly increase during overcharging. The experimental results clearly indicate that the microstructural changes of the separator are important in the above‐mentioned phenomenon.