Due to the rapid compression and the Joule-Thompson effect of hydrogen during fast filling process, the internal temperature of the cylinder rises sharply, which may lead to hidden safety hazards. In this study, a mathematical model of a cascade storage system was developed to analyze the temperature rise in hydrogen cylinders under different working conditions. Results show that the pressure switching coefficient of the cascade storage system has a significant effect on the filling time, and the pre-cooling of hydrogen has a significant impact on the final temperature and the states of charge (S_OC) of the cylinder. Based on these results, a multi-objective optimization algorithm was proposed to optimize the above two controllable variables, taking filling time, energy consumption and S_OC within cylinders as optimizing objectives. The results show that the optimized method can significantly decrease the energy consumption, improve S_OC and allow acceptable refueling time.