Actuator saturation is an important issue when designing practical control systems. It usually induces the windup phenomenon and even yields system instability. In this paper, a two-stage controller design method is proposed for systems with actuator limitations using the loop shaping approach. In this approach, a pre-designed controller is first used to stabilize the control system to achieve the desired performance. A loop-shaping-based auxiliary controller is then introduced to reduce the windup effect, which might be caused by actuator limitation or functional damage during the mission.