A control system structure for the underwater docking procedure of an Autonomous Underwater Helicopter (AUH) is proposed in this paper, which utilizes acoustic-inertial-optical guidance. Unlike conventional Autonomous Underwater Vehicles (AUVs), the maneuverability requirements for AUHs are more stringent during the docking procedure, requiring it to remain stationary or have minimal horizontal movement while moving vertically. The docking procedure is divided into two stages: Homing and Landing, each stage utilizing different guidance methods. Additionally, a segmented aligning strategy operating at various altitudes and a linear velocity decision are both adopted in Landing stage. Due to the unique structure of the Subsea Docking System (SDS), the AUH is required to dock onto the SDS in a fixed orientation with specific attitude and altitude. Therefore, a particular criterion is proposed to determine whether the AUH has successfully docked onto the SDS. Furthermore, the effectiveness and robustness of the proposed control method in AUH's docking procedure are demonstrated through pool experiments and sea trials.