In this paper, a new switched modified function projective synchronization(SMFPS) problem of chaotic system and the application in secure communication is researched.Based on Lyapunove stability theory and active control method, nonlinear feedback controller and the parameters update laws were presented for the switched modified function projective synchronization(SMFPS) between two identical hyperchaotic system with completely unknown parameters.Then this method was applied to secure communication through chaotic masking . The information signal, through function transformations,was masked by the state variables of the drive system and sent to the receiver as a drive signal, then the information signal was recovered at the receiver by eliminating the scaling function and the anti-function transformation. The control strategy had stronger security and practicality. The corresponding numerical simulations demonstrated the effectiveness of the proposed methods.