In this paper, a Hardware-in-the-loop (HIL) simulation method for multiple fuel cells hybrid power system based on field-programmable gate array (FPGA) + CPU architecture is presented. This paper is aiming to propose a parallel modular computing strategy in FPGA, which is used to reduce the programming difficulty and single-step simulation time. In this strategy, different modules are modeled inside FPGA separately and are connected together to achieve the desired circuit by an interactive connection module. In this way, complex programming is not required when building a system. It only needs a combination of different modules, just like building blocks or modeling in Simulink. This strategy can reduce the programming difficulty greatly when developing complex models in FPGA. Furthermore, it is highly parallelizable to achieve a single-step simulation time of 0.1 mu s in FPGA. The simulation and experimental results demonstrate that the HIL simulation platform has the advantages of high speed, high precision, low cost, and easy to popularize.