Water bird is an indicator of a healthy wetland ecosystem. It has been affected more and more by human activities recently. The research, which focuses on environmental suitability change of its habitat in the nature conservative area, may help restore the wetland to some extent. In this paper, we determined the proportion of each factor that may affect the habitat of water bird through the Analytic Hierarchy Process and established an index model for its habitat suitability. According to TM remote sensing images and historical data, we calculated the habitat suitability index of the Shengjinhu National Nature Reserve in five years, from 1986 to 2011. Besides, we analyzed the suitability change of its habitat after the establishment of the natural reserve, combined with the habitat suitability classification map using GIS spatial analysis. The results showed that its habitat suitability was relatively stable in the early years after the establishment of natural reserve in 1986, whereas an obvious decrease was also observed. The habitat suitability began to deteriorate significantly in the late 1990s. The situation lasted until the year 2000, after when it was improved slightly. The districts which had the best habitat suitability were gradually changing from scattered plate-like area to aggregated small range. Suitable area was also obviously reduced during the migration from the experimental and buffer area to the core area. The most suitable areas gradually evolved into suitable areas, while regular suitable region was mainly composed of a suitable area to change, mini-suitable and not suitable for area also increased year by year. Moreover, we discussed imperfections of this research, and provided several suggestions on protecting and rebuilding the habitat suitability of water bird.