Aerial cameras play an important role in obtaining ground information. However, the complex and changeable aviation environment limits its application. Thermal control is vital in improving the environmental adaptability of the camera to obtain high-quality images. Conventional thermal control of aerial cameras is to directly implement active thermal control on the optical system, which is a single layer thermal control method. Such a method cannot isolate the optical system from the external environment. It results in a sharp increase in thermal control power consumption and in temperature gradient, which increases the difficulty of thermal control. Here, we propose a multilayer system-level thermal control approach by partitioning the aerial camera into two parts, i.e., the imaging system and the outline cabin. Two parts are connected by materials with poor thermal conductivity, and an air insulation interlayer is formed in between. Theoretical analysis is carried out to model the internal and external thermal environment of the aerial camera in a complex high-altitude environment. We study passive thermal control of the thermal insulation layer of the outline cabin, the optical window, the imaging optics, the CCD device, and the phase change material, and active thermal control of the thermal convection and heating film. Numerical modeling on the multilayer thermal control of the system is carried out and verified by the thermal equilibrium test and actual field flight test. The total power consumption of the thermal control system is 270 W. High-quality images are obtained when the temperature gradient of the optical lens is less than 5°C and the temperature of the CCD is lower than 30°C. Our technology is simple, accurate, low cost, and easy to implement compared to the conventional thermal control method. It effectively lowers the power consumption and reduces the difficulty of thermal control.