High altitude airships possess tremendous potential for long-endurance spot hovering platforms for both commercial and strategic applications. The energy system, which is mainly made up of solar array and regenerative fuel cell, is the key component of a high altitude airship. The thermal effect is a major factor that affects the performance of the energy system of long endurance stratospheric vehicles. In this paper, a conceptual design method focusing on the thermal and power characteristics of an energy system for stratospheric airships is proposed. The effect of thermal behavior of solar array on the energy system is analyzed. An optimized case is obtained on the consideration of power supply, thermal behaviors of helium and solar array. Results show that the maximum temperature difference of the solar array may be reduced by about 20 K and the mass of payload can be improved by up to 5%.