To understand the spatial and temporal distribution of wind and wave in Lake Taihu, wave observatory was set up in the center of lake. It was found that SWAN model could simulate the waves well in Lake Taihu by using the wave data recorded. Based on the calibrated model, waves of different seasons in Lake Taihu were simulated under the natural wind conditions in 2013. The results showed that due to shoreline, topography and islands, waves in the large Taihu water always showed the strongest with the mean significant wave height of 0.523m, while waves in east Lake Taihu were the smallest with the mean significant wave height of 0.305m. The values of mean significant wave height were higher in spring and summer than in autumn and winter because of seasonal changes. Wave energy in Lake Taihu was driven mainly by wind, leading to the significant wave height increased with wind speed. A significant positive correlation was found between significant wave height and wind speed. The wind direction affected growth and extinction of waves with changing the length of wind fetch. Under the easterly wind, waves in western lake was greater than that in eastern lake; while under northerly wind in winter, waves in southern lake was greater than that in northern lake. Meanwhile, the spatial and temporal distribution of waves was one of the major reasons to form a different spatial distribution of water quality, sediment and aquatic macrophytes in Lake Taihu.