Abstract: The Taihu Lake region is the most developed agricultural region in China. In recent years, driven by economic interests, the transformation of rice paddy into orchard, vegetable field and tea garden in Taihu Lake region has become prominent. The changes in the trend and distribution characteristics of planting structure, as well as the N and P fertilizer inputs and runoff loads (before and after the change in planting structure) are still not studied. Based on the Agricultural Statistical Yearbook and survey data of literatures, through the analysis on planting areas of rice paddy, orchard, vegetable field, and tea garden in major cities in Taihu region (Changzhou, Wuxi, Suzhou, and Huzhou) from 2002 to 2017, nutrient input and N and P loads in farmland were studied to provide scientific basis for prevention and treatment of agricultural non-point source pollution in the area. The main results were summarized as follows: from 2002 to 2017, the planting areas of orchard, vegetable field, and tea garden significantly increased; especially for orchard (increased by 2.852×10⁴ hm²) and tea garden (increased by 1.892×10⁴ hm²). However, the area of rice paddy was decreased by 1.985×10⁵ hm²; the change in rate of planting structure from 2002 to 2010 was much higher than that of 2010 to 2017. The increased planting areas of orchard, vegetable field, and tea garden were mainly concentrated in the lakeside districts, such as Wujin, Nanxun, Yixing, Suzhou urban area, and Changxing. The total N and P fertilizer inputs were decreased by 25.26% and 9.59%, respectively, from 2002 to 2017. The risk of total N runoff reduced significantly by 34.66%, while the total P loss amount remained stable (overall decline by 1.84%). In 2017, the estimated N loss loads from the sources of rice paddy, orchard, vegetable field, and tea garden were 10 200 t, 670 t, 10 100 t and 250 t respectively, and the P loss loads were 290 t, 400 t, 3 000 t and 50 t, respectively, in the Taihu Lake region. With the change in planting structure, rice paddy was no longer the largest source of N and P loss in the farmland, but the total N and P loss from orchard, vegetable field, and tea garden was the largest; these are currently the priority control objects of N and P loss in farmland of the Taihu Lake region. It is suggested that in the next stage, the prevention and control of agricultural non-point source pollution should focus on the optimization of planting structure, and strengthen research on the prevention and control technology of P pollution, in order to achieve clean and sustainable development of the planting industry in the Taihu Lake region.