Satellite Thermal Control subsystem has the responsibility of maintaining the temperature of different parts and other subsystems in an allowable range. The purpose of this paper is to optimally design the satellite thermal control subsystem. In order to achieve this goal, at first a software for thermal analysis of satellite was developed and validated. Receiving orbital data and Satellite’s properties, the software simulates the position of the satellite in any desired orbit and calculates input and output thermal flux. Meanwhile, the software calculates the temperature of each sides of satellite in cold case and hot case. At the end, it computs the minimum and maximum temperature of the satellite. Combination of three commonly used thermal control methods for small satellite was used. Insulation thickness, thickness of radiator’s cover, and the power of radiator are considered as design parameter and allowable temperature of surfaces (minimum and maximum allowable temperature) are considered as design constraints. A weighted function of mass, cost, and power consumption of thermal control system are chosen as objective function that can be an indicator of the cost. Sequential Quadratic Programming as a powerful method in nonlinear optimization was used to optimize thermal control properties.The results demonstrated that the objective function improved dramatically comparing to initial design. High speed, appropriate precision, and extensibility of this software to thermal control design of vast majority of small satellites, makes this research superior. Therefore, this software could be cooperated as the thermal control design module in multidisciplinary design optimization of satellites.