The simulation of formation control models has became an indispensable part of the design of multi-UAV formations. However, when the scale of UAV is large, the time-consuming problem of the simulation is outstanding. In response to this problem, this paper discussed a parallel simulation method based GPU and optimized the CUDA program. The method firstly splits the model into some sub-models, which will be solved on different simulators with GPU. The simulation results verify the correctness and efficiency of the method, and also verify the advantages of the GPU in large-scale matrix operations, and with the increase of scale, the advantages become more and more prominent.