In order to solving traditional controlling problems of being difficult in performance, a three-dimensional fuzzy controller is designed. Introduce the design scheme and designing Ke, Kec and Ku based on choosing expression variables in and out, ensure subjection function of language values and establishing rule table of fuzzy control. A three-dimensional fuzzy controller applied to aerodynamics missile system is designed, which adopted the strategy of subsection control. The results of simulation demonstrate that the controller has such advantages as quick response and no over adjusting control. The track ability of the system is still improved, and the controller reaches the request of the system performance indexes.