Proton exchange membrane fuel cell (PEMFC) stacks are assembled by numerous bipolar plates (BPPs) and membrane electrode assemblies (MEAs). Component manufacturing errors are inevitably caused during the production process and brought into the stack, affecting the mechanical consistency of every cell. Aiming to improve the uniformity of the assembled stack effectively, this paper establishes a novel assembly deviation model based on the asymptotic homogenization (AH) method and proposes an assembly sequence optimization approach for the stack with dimensional errors using the genetic algorithm. The results reveal that dimensional errors significantly affect the equivalent mechanical properties of the stack. Reasonable matching of components with different types of dimensional errors is an effective method to avoid the cumulative negative impacts on the mechanical behavior of the stack. Statistically, the optimization of the assembly sequence can improve contact pressure uniformity in a 10-cell stack by more than 9.00%, while reducing the maximum contact pressure by 15.55%. This methodology is also applicable to improving the assembly uniformity of other stacked structures.