The emergence of biological computing based on DNA strand displacement has allowed chaotic systems to have more abundant dynamic behaviors. So far, the synchronization of chaotic systems based on DNA strand displacement has been mainly realized by coupling control and PID control. In this paper, the projection synchronization of chaotic systems based on DNA strand displacement is achieved using an active control method. First, some basic catalytic reaction modules and annihilation reaction modules are constructed based on the theoretical knowledge of DNA strand displacement. Second, the chaotic system and the controller are designed according to the above mentioned modules. On the basis of chaotic dynamics, the complex dynamic behavior of the system is verified by the lyapunov exponents spectrum and the bifurcation diagram. Third, the active controller based on DNA strand displacement is used to realize the projection synchronization between the drive system and the response system, where the projection can be adjusted within a certain range by changing the value of the scale factor. The result of projection synchronization of chaotic system is more flexible, which is realized by active controller. Our control method provides an efficient way to achieve synchronization of chaotic systems based on DNA strand displacement. The designed projection synchronization is verified to have excellent timeliness and robustness by the results Visual DSD simulation.