Two classical fractional-order complex chaotic systems and their projections of the chaotic attractor phase diagram are studied in this paper. The phase diagram proves the validity of the nonlinear chaotic characteristics of the system. What is more, an active misalignment synchronization controller based on Fractional-order System Stability Theory is proposed in this paper. Finally, numerical simulation results indicate that the proposed active controller could realize the misalignment synchronization between different complex chaotic systems.