Farm ponds in Yunlin County first appeared in 1,622 and have played roles in habitation, production, the ecology, culture, and disaster reduction. Farm ponds largely disappeared with the development of urban areas and the industrial sector; thus, effective preservation of the remaining ponds is critical. The criteria to evaluate the preservation value of farm ponds is established by expert questionnaires which follow the Fuzzy Delphi Method (FDM) and Fuzzy Analytic Hierarchy Process (FAHP), and GIS, which are integrated into a spatial analysis of the remaining 481 farm ponds in Yunlin County. The results show that 28 ponds should be preserved to continue the cultural interaction between farm ponds and settlements; 36 ponds should preserved to connect coasts and streams, which are important habitats for birds; 30 ponds should be preserved to increase storage capacity, recharge groundwater, and reduce land subsidence; four ponds should be preserved as Feng-Shui ponds in front of temples in settlements or as recreation areas for local citizens; and four farms should be preserved (high priority) in agricultural production areas to support irrigation. In short, FAHP and GIS are integrated to evaluate the number and locations of farm ponds that provide water for habitation, production, the ecology, culture, and disaster reduction and maintain the overall preservation value in Yunlin County. The results could inform governmental departments when considering conservation policies.