A fractional differential controller for incommensurate fractional unified chaotic system is described and proved by using the Gershgorin circle theorem in this paper. Also, based on the idea of a nonlinear observer, a new method for generalized synchronization (GS) of this system is proposed. Furthermore, the GS technique is applied in secure communication (SC), and a chaotic masking system is designed. Finally, the proposed fractional differential controller, GS and chaotic masking scheme are showed by using numerical and experimental simulations.