The microporous layer plays an important role in the transmission of water, gas, heat and electricity in proton exchange membrane fuel cells,The deformation and microstructure damage under mechanical stress will seriously affect the transmission. The relationship between stress and strain is first obtained experimentally after fabricating the microporous layer and characterizing its microstructural properties. Then, the microstructure of the microporous layer is reconstructed numerically based on the microstructure characteristic parameters obtained from the experimental characterization. The displacement-stress distributions of carbon particles and polytetrafluoroethylene under different mechanical strains are obtained using finite element method. The results show that the mechanical action causes significant strain to the microporous layer microstructure of PEMFC, and strain located on the microporous layer surface is maximum, which is more likely to produce stress concentration. With the increase of mechanical strain, the stress increases exponentially in the direction of stress. When the strain is 10%, the maximum stress on carbon particles and PTFE is about 31.385 MPa and 14.873 MPa. When the strain increases to 40%, the maximum stress becomes 160.03 MPa and 96.165 MPa, and the stress concentration is the most obvious. The stress concentration area in the microporous layer will obviously increase with the increase of strain.