In this paper, we study how polyolefin separators respond to compressive stress, which can occur during battery operation as active particles lithiate, expand, and push into and deform the separator. We use real microstructures of polyethylene and polypropylene separators acquired with focused ion beam scanning electron microscopic (FIB-SEM) tomography and simulate how these structures deform under compressive strain. After validating our mechanical simulations, we characterize how the microstructural properties of the separators change as a function of compressive strain and simulate the influence these changes in microstructure have on the lithium ion transport through the separator. We find that a given compressive strain negatively impacts the microstructure of polyethylene separator more than that of a polypropylene separator. To understand the origins of the different response to compressive strains in polyethylene and polypropylene separators, we use a network-based analysis to assess the type of mechanical deformations occurring in the separator membrane and show that it is the combination of material properties and structure that are responsible for the greater stability of polypropylene. This work highlights how the structure of a separator plays an important role in its mechanical robustness and prevention of cell degradation. (C) The Author(s) 2018. Published by ECS.