The increasing frequency of natural disasters means that cultural heritage conservation must consider both the local environment and potential impact of extreme weather events. Most suggestions for disaster management regarding cultural heritage in Taiwan ignore the integrity of the environment, with the consequence being that many cultural heritage sites in Taiwan remain threatened by disaster events. Wang (2015) conducted the first mapping survey in Taiwan that concentrated on “static-structural risks” regarding cultural heritage. The present study continues the above one, with adopts a risk-identification perspective with flood as the main disaster type, and enlarges to a regional scale operation and analysis. This study analyzes the categories and amounts of cultural heritage that might suffer from disasters based on a geographic information system that integrates flooding susceptibility data with cultural heritage sites. Through searching the possible flooding causes and impact factors, hoping to provide the information serves to inform the measures of future risk mitigation and disasters reduction efforts. The results reveal that heavy rain is an important issue that needs to be addressed for cultural heritage. The sites most impacted by floods were as follows (most to least): historical buildings, municipal and county monuments, national monuments, and archaeological sites, whereas traditional settlements and cultural landscapes are not impacted. The reason these sites are not affected might be due to their altitudes or the local knowledge of those who built the sites. Changes in the local environment, such as land subsidence and terrestrialization, are also important factors that affect whether cultural heritage are affected by floods. In the future, for disaster management of cultural heritage, it is necessary to conduct cross-disciplinary professional integration and comprehensively use structural and non-structural disaster reduction measures to reduce the disaster vulnerability of cultural heritage and strengthen its resilience after considering regional and cultural heritage characteristics.