Taking into account various heat transfer modes inside and outside the fuel tank, a set of differential equations for thermal balance covering the tank wall, the gas inside the tank and the fuel was established. A universal fuel tank thermal simulation model was developed based on the Amesim software. Based on the fuel tank thermal model, a thermal simulation platform for the fuel system of a high-altitude long-endurance unmanned aerial vehicle (HALE UAV in short) was built, and dynamic thermal simulation analysis and temperature control strategy research during flight were carried out. By comparing with the measured data from flight tests, it was verified that the established fuel system thermal simulation platform has high credibility. Based on the platform, the fuel temperature distribution characteristics at each node of the traditional fuel system were analyzed. The research results show that the fuel temperature at the engine inlet is the key factor limiting the improvement of the system"s heat dissipation capacity, while the fuel temperature in the left and right fuel tanks restricts the low-temperature endurance performance. The traditional scheme has the dual problems of insufficient heat dissipation capacity under high-temperature conditions and fuel temperature lower than the low-temperature limit under low temperature conditions. Quantitative analysis shows that under given mission profiles and heat dissipation loads, in-creasing the return fuel flow can effectively reduce the fuel temperature at the engine inlet. When the return fuel flow increases from 0.1kg/s to 0.3kg/s, the maximum fuel temperature at the engine inlet drops from 68.5℃ to 54.5℃. But the change in return fuel flow has no significant effect on the fuel temperature in the left and right fuel tanks. To solve the above problems, a temperature control strategy of returning fuel to the current fuel tank being supplied was innovatively proposed. Under the premise of maintaining the given fuel supply sequence, this strategy significantly improves the system"s heat dissipation performance and the fuel temperature in the left and right fuel tanks. Compared with the traditional system, this strategy increases the heat dissipation capacity under high temperature conditions by 133.7%, and raises the final fuel temperature in the left and right fuel tanks under low temperature conditions by 18.7℃, and enhances the cold endurance capability by 166.1%. This research provides important support and design reference for the temperature control and comprehensive thermal management of the fuel system of HALE UAVs.