A designing method of fractional order internal model controller is proposed for complex systems. Firstly, the model is reduced by using the particle swarm optimization(PSO) algorithm. Then a fractional order controller is designed based on the principles of internal model control(IMC). The controller has only one adjustable parameter. Moreover, according to a robustness index, the analytical expression of controller parameter tuning is given. The simulation results show that the fractional order internal model controller can provide a better dynamic performance of both the command tracking and disturbance rejection and a better robustness against the parameters perturbation of the system.