To the problem that traditional control method for quality controlling is sensitive to the change of aerodynamic parameters, an improved fractional order controller was designed based on fractional order calculus theory and Linear Quadratic Regulator (LQR) optimal control technique.First, state reconfiguration of missile dynamics model was carried out, by using LQR technique and output feedback, a three-loop control structure based on missile optimal tracking index was obtained.Then, a generalized fractional order controller structure was constructed.Parameters of the missile fractional order controller were tuned by an improved particle swarm optimization algorithm, in which both the performance in time domain and frequency domain stability performance and penalty function were combined to construct a fitness function.The controller parameters were set though Particle Swarm Optimization (PSO) algorithm.Simulation results show that the fractional order controller has a good steady and dynamic performance.