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It is complicated to set parameters of fractional order PID controller, the optimization results from traditional method are not only difficult to achieve but poor, so this paper put forward an improved artificial colony algorithm to complete the fractional order PID controller’s parameter setting. First, improving the searching equation and adding an elimination mechanism in artificial colony algorithm to achieve parameters’ intelligent searching. Next those parameters will be sent to the fractional order PID controller and then repeat forementioned process. Meanwhile, using the integral of absolute error index (AIE) with weights as the objective function. Finally the controller can be concluded. This paper used a nonlinear system as a controlled object, by simulation and analysis, proved the controller’ performance of improved algorithm is more better in dynamic and steady-state than the controller of traditional integer order and the controller without improved artificial colony algorithm.In addition, this new algorithm we proposed is better than not improved algorithm in the aspect of maximum overshoot, rise time and oscillation.