A preliminary phytoplanktonic index of biotic integrity (P-IBI) was developed to evaluate the ecosystem health of Taihu Lake in winter by means of the data that were collected from 29 sites in Taihu Lake and 4 sites in similar lakes or reservoirs in December 2012. The method of the least disturbed condition was used to find the reference sites. Fifty-one metrics were examined stepwise in the distribution analysis, discriminating power analysis, and redundancy analysis to obtain the core metrics. The final P-IBI included the total taxa number, Bacillariophyta taxa number (%), the Simpson diversity index of cells, cell density, Bacillariophyta cell density(%), and Chlorophyta individual density (%). These metrics were transformed into uniform scores using the ratio score method, and a P-IBI value was obtained by summing up the scores. According to the P-IBI assessment, 8 reference sites included 1 healthy site, and the rest were subhealthy; 2 of 25 impaired sites were subhealthy, while 9 were good-to-fair, 12 were fair, and the other 2 sites were poor. East Taihu Lake was best in terms of the health condition in the entire Taihu Lake, while the central region was the worst. The health conditions in other regions (Zhushan Lake, Gong Lake, eastern lakeshore, and western lakeshore) were intermediate, meaning relatively poor conditions. Our results suggest that ammonia nitrogen and total phosphorus are the major factors that correlate significantly with the P-IBI score for Taihu Lake in winter.