The structural changes of polyolefin separator during its service life greatly affect the working efficiency and safety of the lithium-ion battery. Researchers have known little about the relationship between the structural change of the separator and battery performance aging during the service cycle. Therefore, we design one device that could simulate the separator environment in the battery to track the separator structure evolution during the periodic deformation process. In this work, the polypropylene separator is chosen and 1-, 50- and 100- cycle compression tests are carried out saturated with dimethly carbonate at different compression strain 7.5%, 12.5% and 15%. The separators show different degree of transparent wrinkles on the surface and higher impedance as the strain increases. The ionic conductivity becomes lower. The discharge capacity declines by 32.2% in DMC-12.5% and by 46.3% in DMC-15%. The voltage platform of charge and discharge in DMC-15% reduce obviously. The damaged degree of lamellae skeleton around the transparent wrinkles in the separator is increased with the cycle times and compression strain. Along the transverse direction, some pores are compressed and even closed, leading to the appearance of transparent wrinkles on the separator surface and resulting in the worse electrochemical performance.