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Fuel cell vehicle commercialization and mass production are challenged by the durability of fuel cells. In order to research the durability of fuel cell stack, it is necessary to carry out the related durability test. The performance prediction of fuel cell stack can be based on a short time durability test result to accurately predict the performance of the fuel cell stack, so it can ensure the timeliness of the test results and reduce the cost of test. In this paper, genetic algorithm-BP neural network (GA-BPNN) is proposed to modeling automotive fuel cell stack to predict the performance of it. Based on the strong global searching ability of genetic algorithm, the initial weights and threshold selection of neural networks are optimized to solve the shortcoming that the random selection of the initial weights and thresholds of BP neural network which can easily lead to the local optimal value.