In this paper, fuzzy Petri Net controller is used for Quadrotor system. The fuzzy Petrinet controller is arranged in the velocity PID form. The optimal values for the fuzzy Petri Net controller parameters have been achieved by using particle swarm optimization algorithm. In this paper, the reference trajectory is obtained from a reference model that can be designed to have the ideal required response of the Quadrotor, also using the quadrotor equations to find decoupling controller is first designed to reduce the effect of coupling between different inputs and outputs of quadrotor. The system performance has been measured by MATLAB. Simulation results showed that the FPN controller has a reasonable robustness against disturbances and good dynamic performance.