Since the dynamical system and control system of the missile are typically nonlinear, an effective acceleration tracking autopilot is designed using the dynamic surface control (DSC) technique in order to make the missile control system more robust despite the uncertainty of the dynamical parameters and the presence of disturbances. Firstly, the nonlinear mathematical model of the tail-controlled missile is decomposed into slow acceleration dynamics and fast pitch rate dynamics based on the naturally existing time scale separation. Secondly, the controller based on DSC is designed after obtaining the linear dynamics characteristics of the slow and fast subsystems. An extended state observer is used to detect the uncertainty of the system state variables and aerodynamic parameters to achieve the compensation of the control law. The closed-loop stability of the controller is derived and rigorously analyzed. Finally, the effectiveness and robustness of the design is verified by Monte Carlo simulation considering different initial conditions and parameter uptake. Simulation results illustrate that the missile autopilot based DSC controller achieves better performance and robustness than the other two well-known autopilots. The method proposed in this paper is applied to the design of a missile autopilot, and the results show that the acceleration tracking autopilot based on the DSC controller can ensure accurate tracking of the required commands and has better performance.