A new controller design method was proposed to synchronize a class of fractional order chaotic system through the stability theory of fractional calculus. In order to make effective synchronization between two fractional order systems, one suitable controller need to be added to the system only. In order to improve the system of communication security and the implementation of the secure transmission of complex aperiodic information, the scheme was applied to chaos masking secure communication based on chaotic communication technology. The useful information was properly recovered at the receiver through chaos unmasking. Finally, numerical simulations as well as the theoretical analysis were provided.