To achieve better understanding on degradation phenomena of PEMFC, the mechanism of microstructure changes in catalyst layer urgently needs to be understood. To this end, the mechanical analysis is implemented to understand the underlying mechanism of microstructure changes in this work. To understand the mechanical mechanism of microstructure changes in catalyst layers caused by cycling of start-up and shutdown during the operation of a PEM fuel cell, and to recur the nature of microstructure, the initial random microstructure is reconstructed based on the statistical information of experimental figures of practical catalyst layers. In addition, the material model, combined with the cohesive zone model and the contact model, is solved using the available finite element method. The cohesive zone model and the frictional contact model are used to describe the evolution of interfaces between protonic and electronic conducting phases. The numerical simulation shows that there is a competition between crack initiations in bulk material of protonic phase and delamination between different phases. This competition plays an important role in microstructure changes in catalyst layers. Although different reconstructed microstructures have various changes, one common indication on performance degradation is observed that connection length of different solid components in catalyst layer decreases after certain duty cycles of PEM fuel cell.