The ecological environment problem is the fundamental problems affecting human survival and development of social economy. In recent years, with the emergence of a series of environmental problems such as global warming, air pollution, soil erosion, lack of fresh water resources and so on, it has been known gradually that a good ecological environment is one of the necessary conditions for existence and development of human being. By using GIS and RS technology, the basic data were processed in order to extract the matic information. Moreover, a comprehensive evaluation using comprehensive index model was established based on the full understanding of the characteristics of the ecological environment of the Quanzhou Bay area. Research shows that the ecological environment of Quanzhou Bay area is good in general. In every rank as the five level of division, the third grade above area accounts for 86.81%.The second grade has the highest proportion, leading the level of whole situation for regional ecological environment. But there is still poor partial district in need of attention. It also shows that the theory and method of comprehensive evaluation on ecological environment based on GIS and RS technology has a strong exploratory and pioneering: using GIS and RS method for the comprehensive evaluation of the regional ecological environment, the data acquisition has the characteristics of convenient and fast. Raster overlay function can make the evaluation results more accurate. Spatial expression function can make the evaluation results more direct viewing and more likely to accept.