While reducing the size and Pt loading can achieve a lower proton exchange membrane fuel cell (PEMFC) stack cost, it is also very important to focus on the performance changes of the PEMFC stack during the long-term operation. A 3D PtCo catalysts long-term performance model is established in this study, and PEMFC stacks with one cooling unit per cell (1-cell stack) and three cells (3-cell stack) are employed as the computational domains, respectively. The effective area of each cell is 50 cm2, and the changes in current density as well as effective catalytic area of PEMFC stacks with two cooling strategies before and after long-term operation under different humidity conditions are investigated at low Pt loadings. The results show that there are large differences in the output voltage and current density distributions between the three cells due to the poor membrane hydration affected by the non-uniform temperature distribution, although the 3-cell stack can significantly reduce the size. Localized catalyst degradation in both 3-cell and 1-cell stacks is closely related to the geometry of the cathodic flow field, and non-uniform catalyst degradation is found to increase the activation and mass transfer losses and change the distribution of current density within the membrane. In addition, the 3-cell stack is found to perform even better in terms of durability, especially under high humidity conditions, which provides a potential solution to improve the durability of PEMFC stacks operating in harsh conditions.