Underwater cultural heritage (UCH) contributes to history, the arts, the economy and science. The number of intact and easily discoverable UCH sites is decreasing due to excavation in China. To conduct active surveys for mapping archaeological sites, rather than mapping based only on incidental reported finds from fishing operations, a regional archaeological underwater survey method is proposed according to independent geographical units and historical archives. This method is based on the approach used for systematic regional archaeological surveys on land and comprehensively examines similar survey examples. Old port districts, sea routes, fishing zones and naval battle areas are potential targets for this method. From 2012 to 2017, the survey method performed well when applied in the Haitan Strait, China, discovering intact sites, fragmented shipwrecks and numerous interfering objects. The method needs further refinement to eliminate interference and to obtain more detailed information about UCH. The main steps in this method include the selection of potential wreck site areas, the use of sequential equipment and survey line design. Cooperation between archaeologists and surveyors is essential.