In order to improve the security of secure communication, a new Generalized Hybrid Dislocated Function Projective Synchronization (GHDFPS) based on generalized hybrid dislocated projective synchronization and function projective synchronization was researched by Lyapunov stability theory and adaptive active control method. At the same time, the control methods of GHDFPS between two different-order chaotic systems with uncertain parameter and parameter identification were presented, and the application of the novel synchronization on secure communication was analyzed. By strict mathematical proof and numerical simulation, the GHDFPS between two different-order chaotic systems with uncertain parameter were achieved, the uncertain parameter was identified. Because of the variety of function scaling factor matrix, the security of secure communication has been increased by GHDFPS. Moreover, this synchronization form and method of control were applied to secure communication via chaotic masking modulation. Many information signals can be recovered and validated.