Due to the single-side heating on the rectangular channel, the coolant faces a serious thermal stratification problem, and thus the heat transfer performance is reduced. To effectively improve flow and heat transfer characteristics, and weaken nonuniform distribution problem, a new cooling structure with combining fin and spherical convexity is built in this paper. The study results indicate that the new structure effectively reduced the maximum heat wall temperature, and weakened the fluid nonuniform distribution problem. Comparing with smooth channel and spherical convexity structure, the maximum temperature is decreased by 18.4% and 10.3%, and temperature nonuniform index is decreased by 25.1% and 20.8%. In addition, as the higher fluid temperature means the higher specific heat capacity, the new structure made full use of the heat sink of hydrogen, making the more heat can be quickly taken away from the heat wall. The thermal stratification phenomenon can be obviously weakened.