The automatic flight control system of civil aircraft plays a vital role in enhancing flight safety and alleviating the pilot’s workload. The control laws and switching logic of the modes 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 was provided in this study. By designing the control laws and establishing a rational mode switching mechanism, aircraft safety and control stability under different flight modes were guaranteed. First, to meet the longitudinal and lateral control requirements of the automatic flight system, load factor (N_z) and roll rate-sideslip angle (p-β) command tracking control was adopted in the inner loop to ensure stable flight and precise attitude control in different modes. The outer loop incorporated gain adjustment and feedback mechanisms to optimize the aircraft’s responsiveness and stability, further improving the handling accuracy during flight. Regarding the mode switching logic, a mode switching scheme based on the finite state machine theory was proposed in this research. A state machine model for longitudinal and lateral mode switching was 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 enhance human-machine interaction performance, a new human-machine interface was designed, through which the pilot can input commands, perform mode switching, and set target values. Simulation results show that the proposed control laws can precisely track the desired N_z and p-β commands, that the transition between different operational modes is smooth and safe, and that the automatic control requirements during the cruise phase are satisfied.