Bay ecosystem health, recently, has faced a growing interference and disturbance by anthropogenic activities, which has also caused challenges to ecosystem management. Ecosystem health assessment, a new methodology of ecosystem assessment, could obtain the current situation both of ecosystem structure and function and provide a great of necessary information for ecosystem management. An integrated assessment methodology for bay ecosystem health was established based on geographical information system (GIS) technology, which was on basis of a "pressure-structure-response" frame model for marine ecosystem and an ecosystem health assessment indicator system constructed by external pressure, ecosystem structure and response parameters. This paper also presented a case study of Daya bay in spring by employing GIS technology.The results showed that the average ecosystem health integrated index was 0.57 in Daya Bay ecosystem in spring. Detailedly, organic pollutant index ranged from 0.36 to 1, with the average value at 0.87, was at "very good" level of Daya Bay ecosystem. Eutrophic level index value ranged from 0.17 to 1, with the average of 0.77, indicated "better" level of the ecosystem. Furthermore, phytoplankton abundance index was at a "worse" level because of the ranges from 0.33 to 1 and the average of 0.21. Zooplankton biomass index ranged from 0.16 to 1, with the average of 0.88, suggested the ecosystem was at a "very good" level. Zoobenthos biomass index was at "critical state", as the index value ranged from 0 to 1 and the average value at 0.59. Moreover, phytoplankton diversity index was also "critical state" level, as the index ranged from 0.39 to 0.75 and the average of 0.55. Primary productivity index, ranged from 0.21 to 1 and the average of 0.77, illustrated the "better" level of the ecosystem. However, ecological buffer capacity index was at a "worst" level, as the index value ranged from 0 to 0.39 and the average value of 0.06. Resumptively, spatial distribution of the assessed sea area could be divided into three zones according to the grade of integrated assessment index, namely "good health zone", "critical health zone" and "bad health zone". The percentages of three zones were 46.56%, 47.97% and 5.47%, with the average integrated health index of 0.64, 0.54 and 0.35, respectively.In general, the status of the Daya Bay ecosystem health was at a "better" level according to the above indexes. However, the health status of the ecosystem was potential to change to "critical state" by the negative influences by factors including phytoplankton abundance, phytoplankton diversity and buffer capacities of the ecosystem. The "bad health zone" in the Daya Bay ecosystem distributed at or near the area with the intensive anthropogenic activity. Consequently, the special distribution of Daya Bay ecosystem health status was mostly affected by anthropogenic activity around the bay. The established methodology has been ultimately proved to be a valuable quantitative assessment method and to be worth widely popularizing in marine ecology due to the characteristics of wide applicability, high accuracy and good expression.