Abstract Due to the difficulty of studying nonlinear quantum systems and the unique composition of Bose–Einstein condensate (BEC) systems, BECs face significant difficulties in solving dynamic analysis and chaotic control problems. Therefore, Hartree–Fock mean field theory is introduced to study the chaotic characteristics, control, and synchronization issues of BEC systems loaded on optical lattices. First, the stability and chaos of BECs in optical lattices were analyzed. Subsequently, constant shift method and activation control were introduced based on the Gross–Pitaevskii equation to achieve control and synchronization of the BEC system. Second, based on the Lyapunov exponent theory, offset parameters are added to BEC chaotic control to achieve control of particle density. Finally, based on the stability theory of linear systems, a control term is introduced to achieve variable analysis of the system’s drive–response system, ensuring that chaotic systems with different initial conditions can still achieve good synchronization and anti-synchronization control. The chaotic problem of BEC system was analyzed using numerical and theoretical methods in the experiment. The effect of adjusting the parameters of the BEC system under the constant shift method is significant. The system exhibits a chaotic state under the Lyapunov exponent, which is mainly concentrated between [3.4, 4.5], demonstrating good system stability. When the offset constant range is [4.21, 5.67], the maximum Lyapunov exponent value is below 0. In the problem of chaotic synchronization, adding activation control causes the system’s time series to exhibit anti-synchronization with spatiotemporal variable variation, while adding control terms leads the system to tend towards synchronization and anti-synchronization with time evolution. The analysis of chaotic control problems in BEC systems can provide reference value and theoretical basis for the dynamic research of quantum physics and related nonlinear systems.