To obtain detailed information on the temperature field and thermal stress field inside the solid oxide fuel cell (SOFC) fueled with partially pre-reformed methane. A three-dimensional geometric and mathematical model of the SOFC is implemented by using the finite element method in the commercial software COMSOL Multiphysics®. The coupling characteristics were analyzed for electrode chemical reaction, multi-component mass transfer, and heat transfer process under typical operating conditions, which was further applied for predicting and analyzing the thermal stress distribution. After model validation, parametric simulations are conducted to investigate how the methane pre-reforming percentage and flow arrangement affect the temperature and the thermal stress of SOFC. The simulated results show that reducing the methane pre-reforming percentages can decrease the temperature maximum and the variation range of the first principal stress, but will increase the possibility of carbon deposition. The maximum temperature of the counter-flow is about 20 K lower than that of the co-flow, and the first principal stress variation range of the counter-flow is 8.6 Mpa lower than that of the co-flow. The methane pre-reforming percentages have a significant effect on the heat transfer and the thermal stress, and the counter-flow can improve the temperature uniformity and reduce the thermal stress variation range.