A new method based on least square support vector machines (LS-SVM) is proposed for chaos control of fractional order system. Based on the stability theory of fractional order linear system, the system is decomposed into stable linear parts and the corresponding nonlinear parts. The active controller is designed to compensate the nonlinear parts by using the excellent nonlinearity approximation ability and better generalization capacity of LS-SVM. Thus fractional order chaotic system is suppressed to the equilibrium point. Fractional order Liu system and fractional order Chen system are illustrated respectively. The simulation results verify the effectiveness and feasibility of the proposed method.