Aiming at solving the disturbance problem faced by the mini-missile as well as following practical classic linear frequency-domain design methods, a promoted disturbance estimation and rejection control method based on H_∞synthesis and equivalent-input-disturbance was proposed to apply to the missile longitudinal control system design. The mismatched disturbance problem was resolved by the establishment of equivalent-input-disturbance system. A disturbance filter and a composite controller were designed through H_∞optimization to realize the disturbance estimation and compensation and simultaneously to guarantee the overall stability of the system. The feasibility and effectiveness of the method was validated by numerical simulation and bias comparison with extended state observer based control and disturbance observer based control methods.