In this paper, a genetic programming method for satellite system design is proposed to simultaneously optimize the topology and parameters of a satellite system. Firstly, the representation of satellite system design is defined according to the tree structure. The genetic programming method is designed based on that representation. Secondly, according to the tree structure of different satellite schemes, different multiscale satellite models are established, in which various physical fields couple together. Then, an evaluation system is also proposed to test the performances of different satellite schemes. Finally, the application to the design of an earth observation satellite demonstrates the effectiveness of the proposed method.