Disclosed herein are an underwater docking system and a docking method using the system. An exemplary embodiment of the present invention relates to a system for docking a target body on a docking station under water, the system comprising: a guide unit provided to the docking station to transmit at least one guide signal to the target body; an agent unit connected to the docking station by a smart cable and disposed at a position spaced apart from the docking station so that the agent unit is moored under the water in a direction corresponding to a tidal current; and the target body configured to be guided toward the agent unit by the guide signal and then connected to a portion of the agent unit.