Abstract: Data of chlorophyll-a and other environmental factors from January 2013 to July 2015 in Taihu Lake were sampled. It was found there existed significant difference of water quality in different parts of Taihu Lake. Therefore, the lake was divided into four areas, i.e. Meiliang Bay, Gonghu Bay, Zhushan Bay and Main Lake Area. The generalized additive model (GAM) was introduced to analyze the relationship between chlorophyll-a and nutrients and other environmental factors. The results showed that there was significant nonlinear relationship between chlorophyll-a was total phosphorus (TP) in Meiliang Bay. The relationship between the chlorophyll-a and TP was linear, while the relationship between chlorophyll-a and total nitrigon (TN) was non-linear in Gonghu Bay, and TN was possibly the main limiting factor in the bay. There was significant non-liner relationship between chlorophyll-a and TP and COD_Mn in Zhushan Bay, and COD_Mn was a more significant factor; the reason may be that Zhushan Bay was the key area of organic pollutants emission. Both TN and TP had a strong effect on chlorophyll-a in main area of Taihu Lake and there was significant non-liner relationship between TN, TP and chlorophyll-a. The outbreaks of eutrophication are inconsistent in different areas of Taihu Lake, and the different environmental factors have resulted in different conditions of entrophication.