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Owing to these phenomena about intercalation and deintercalation lithium-ion, thermal expansion, and external pressure in lithium-ion batteries, the interior separators are often subjected to compression stress. In this study, we have designed a novel model based on the Thiessen Polygon, which is used to describe 3D porous structure of polyethylene (PE) separator. It can simulate the structure evolution of separator during compression. The simulation results show that when the compression stress is up to 60 MPa, the thickness of the separator decreases by nearly 50%, and the porosity decreases from 42.6% to 10%, which severely affects the ionic transmission performance. Additionally, the separator with changed porosity structure under different compression conditions was applied to the electrochemistry-thermal model to simulate the discharge process of the battery. As results, it is found that the discharge capacity is significantly reduced and the temperature is increased due to the structural variation of the separator caused by compression stress. This study develops a novel mechanical model which can be used in the simulation of separator compression process, and involves the simulation of multiple physical fields. And it successfully correlates the mechanical properties of separator with its battery performance. • A novel mechanical model of the PE separator has been developed. • The structure evolution of separator during compression has been simulated. • Compressed separator causes degradation of the battery performance. [ABSTRACT FROM AUTHOR]