Abstract: The thermal management of proton exchange membrane fuel cell (PEMFC) is the key factor affecting the safe, stable and high efficient of PEMFC. Based on the structure analysis of the PEMFC thermal management subsystem and its operating principle of key components (including air compressor, coolant circulation pump and cooling fan), a PEMFC simulation model coupling with the thermal management subsystem is created firstly, and it is linearized further to obtain a simplified control orientated linear model. Then, a state observer based on Kalman filtering is designed to estimate the state and non-measurable perturbations, for the purpose of eliminating static errors. To minimize the net output power tracking error and maximize the system efficiency, a target calculator is designed to optimize the state variables of the PEMFC system. Consequently, an offset-free explicit model predictive control (offset-free EMPC) is proposed based on the control orientated linear model to track the optimal state variables. Finally, a kind of software in the loop (SiL) test platform is created. By comparing with the traditional MPC strategy, the SiL simulation results demonstrate that the offset-free EMPC is able to reduce average tracking error of the net output power from 344.29W to 82.19W, the system efficiency is increased from 40.32% to 46.56%, and the strategy single-step average time consumption is reduced from 26ms to 11.8ms. Furthermore, the PEMFC system can be constrained over a stable and safe operating conditions.