In order to solve the problem of unreasonable distribution of coolant flow rate in fuel cell engines, resulting in excessive overall flow rate between the stack and the intercooler, a combination of experimental testing, simulation analysis, and theoretical calculation was used to optimize the flow distribution manifold. Experimental design was carried out to measure the rates of the coolant flow entering into the stacks and the intercooler at different pump speeds. Using a combination of CFD numerical simulation and mathematical modeling methods, the coolant flow rates were redistributed. Taking the distribution manifold structure of a certain fuel cell cooling system as an example, its structure was optimized to reduce the flow rate of the intercooler from 0.73 kg/s to 0.368 kg/s while ensuring sufficient flow rate to the stacks. This study gives some guidelines for the flow distribution design of similar systems in engineering applications.