The automatic flight control system of civil aircraft is critically important for enhancing flight safety and alleviating the pilot’s workload. The mode control law and switching logic of the automatic flight control system are crucial to ensuring flight safety. An in-depth analysis of the mode control and switching logic of the automatic flight control system during the cruise phase is provided in this study. By designing the control laws and establishing a rational mode switching mechanism, the safety and stability of automatic control under different flight modes are guaranteed. First, to meet the longitudinal and lateral control requirements of the automatic flight system, Nz and p-β command tracking control is adopted in the inner loop to ensure stable flight and precise attitude control in different modes. The aircraft’s responsiveness and stability are optimized by the outer loop through gain adjustment and feedback mechanisms, and the handling accuracy during flight is improved. Regarding the mode switching logic, a mode switching scheme based on the finite state machine theory is proposed in this research. A state machine model for longitudinal and lateral mode switching is developed using the Stateflow module, which ensures that the mode transition between different flight stages complies with safety protocols, thus avoiding confusion in the control system. To achieve a more intuitive operation interface, a human-machine interaction interface is designed, through which the pilot can input commands for mode switching and target value setting. Simulation results show that the proposed control laws can precisely track the desired Nz and p-β commands, that the transition between different operational modes is smooth, and that the corresponding control requirements are satisfied.