Aiming at the missile longitudinal motion model with obvious aerodynamic nonlinearity, this paper proposes a two-timescale design method of missile autopilot based on suboptimal control. By dividing the system states into fast and slow states based on different timescales, the corresponding fast and slow control inputs are designed. This paper introduces suboptimal control and robust control to enable the system to have good dynamic response characteristics, and the system’s ability to suppress various uncertainties is guaranteed. By applying the Lyapunov method, the stability conditions of the system are given. Finally, the simulation results show that the system has good dynamic characteristics and robustness.