To address the problem of synchronizing chaotic systems with unknown parameters and complex state variables that cannot be separated, a misalignment complex correction function projection synchronization (MCCFPS) control scheme is proposed. First, an adaptive tracking controller is designed to accommodate the differences between any bounded complex chaotic systems. This controller enhances adaptive capability and adjusts convergence speed through dynamic control strength and convergence factors, and proves the convergence of the controller through Lyapunov theory, providing theoretical support for the reliability of the control scheme. Subsequently, the dynamic models of two heterogeneous complex chaotic systems are analyzed. Fuzzy entropy of the time series of chaotic and complex chaotic systems is calculated and compared to validate that complex chaotic systems have higher complexity. This highlights the superiority of their synchronization control in secure communication applications. The MCCFPS synchronization scheme is further designed. Finally, the effectiveness of the MCCFPS scheme is verified through numerical simulations. The results demonstrate that the scheme successfully achieves synchronization control of complex chaotic systems, exhibiting good synchronization effects and control performance. Overall, compared to traditional chaotic systems, this study introduces complex variables and adopts a more sophisticated synchronization control scheme, MCCFPS, to directly achieve chaotic synchronization in the complex domain, effectively enhancing system security. This research provides new ideas and approaches to the synchronization control problem of complex systems, holding significant practical value.