In order to protect the organic relics and fragile relics inside “Yangtze River Estuary II” ancient ship, the ancient ship will be salvaged and transferred to a dry dock. The condition of the salvaged ancient ships is poor, and the requirements for the protection of cultural relics inside the ship are high. The dry dock used is the former abandoned dock which is not in good condition. Based on the analysis of the current situation of the abandoned dock, hydrological data, the timing of docking and comprehensive analysis of ancient ship handling scheme, the process flow of docking under complex conditions is summarized, which also provides a new process idea for subsequent similar projects.