The invention relates to an unmanned ship underwater archaeology control system and method based on bionic fishes. The system comprises an unmanned ship and a bionic fish, wherein the unmanned ship isprovided with a positioning system, a sonar, a control center, a bionic fish throwing and recycling device, a data arrangement module, a first communication module and a first storage module, and ismainly responsible for depth measurement and data fusion storage of an investigation target, and the bionic fish is provided with an inertial navigation system, a high-definition camera, a driving system, a control system, a data analysis module, a second communication module and a second storage module, and is mainly responsible for detection and data screening of the investigation target. According to the invention, the unmanned ship is used as a carrier, and the bionic fish is used as an underwater archaeology investigation target detection main body, so that the problems of limited sinkingdepth and limited underwater operation time can be effectively solved, the risk and personnel cost of underwater archaeology investigation work are reduced, the investigation range is enlarged, and the investigation efficiency is improved.