Abstract. In order to shorten the design period, and to reduce the cost of unmanned aerial vehicle system design, the design method of complex systems by using virtual prototype technology is studied. Firstly, the design environments of complex system which construct of Rhapsody, Matlab/Simulink, Oracle and VC + +. Secondly, a detailed design process of complex system based on model-driven development was researched. Finally, taking FCS of UAVS for example, a complex system was designed. The simulation results demonstrate that the complex system is feasible, stable, and it can simulate FCS from the architecture, function, behavior, performance and other aspects; support complex software model-driven development; improve the efficiency of the UAVS design.