According to the chaotic communication method and system based on complex modified projective difference function synchronization provided in the present invention, when a chaotic signal has a relatively small amplitude, the amplitude of the chaotic signal can be adjusted by adjusting a proportional matrix, so as to mask plaintext better. Moreover, a robust controller is designed according to a filtered signal and a second coupling function, to ensure complex modified projective difference function synchronization, and such synchronization allows the bit error rate to be zero theoretically. In addition, complex modified projective difference function synchronization does not require a transmitter and a receiver to be exactly consistent, provided that the synchronization can be implemented under the effect of the controller, thereby solving the disadvantage in the prior art that the receiver system and transmitter system are required to have exactly identical structures, and simplifying a structure requirement on the communication system.