For a class of continuous time different structure chaotic systems, due to the strong robustness and adaptability of active disturbance rejection controller (ADRC), we put forward a kind of the anti-synchronization of different structure chaotic systems with auto-disturbance-rejection control strategy. Because there are many parameters in ADRC and they are very difficult to set, in this paper we propose a chaotic particle swarm optimization algorithm to optimize the parameters of controller. Using Lorenz system and Chua system with different structures as an example to perform the simulation test, the results of the simulation verify that the proposed method can realize the anti-synchronization control of the different structure chaos systems faster and has a very strong anti-interference ability.