To study the effect of urea nitrogen on the ecosystem of Lake Taihu, we conducted urea and various nitrogen analysis for the water samples collected from the lake and surrounding rivers during summer. The ecological index analysis of 82 sites in rivers and lake yielded the following results: (1) The urea nitrogen contents in Taihu ranged from 0.011 to 0.161 mg x L(-1), which was high in the northwest and low in the southeast, related to the main pollution sources distribution of its drainage basin. (2) The dissolved nitrogen was dominated by inorganic nitrogen and the ratio between ammonia nitrogen and nitrate nitrogen was 5: 1. The average percentage of urea nitrogen in total nitrogen, dissolved nitrogen, dissolved organic nitrogen and bioavailable nitrogen was respectively 2.28%, 5.91%, 15.86%, and 6.22%, which showed a significant ecological function in Taihu. (3) Urea nitrogen concentration in river was more than twice that in lake, and the lake river concentration was slightly higher than the river into the lake. (3) In Taihu, there was a transformation relationship between urea nitrogen and the nitrogen in other forms. It showed that urea nitrogen had a significant positive correlation with permanganate index and the other forms of nitrogen, and a significant negative correlation with dissolved oxygen. In addition, urea nitrogen was weakly and positively correlated with chlorophyll a, while closely related to the spatial distribution of benthos and zooplankton species. All the results above showed that urea nitrogen was the bridge of organic and inorganic nitrogen transformation, and was the sign of nitrogen cycle of Lake Taihu, which was controlled by the circulating rate. High nitrogen content (especially the organic nitrogen) and low dissolved oxygen content were the key contributors to the increased urea nitrogen content. In Taihu, the urea nitrogen content was affected by both exogenous input and endogenous release.