In order to clarify the characteristics of nitrogen and phosphorus and influencing factors in water-soil-plant system in the riparian zone of the Sunxi River watershed, Chongqing, the descriptive statistics, cluster analysis, correlation analysis and redundancy analysis were carried out to study the characteristics of nitrogen and phosphorus content and spatial distribution in water, soil and plants in the riparian zone of the small watershed at the end of the Three Gorges Reservoir, as well as to study the correlation between nitrogen and phosphorus in each sphere and the factors influencing nitrogen and phosphorus in water. The results showed that:(1) The riparian zone was affected by the river section. From upstream to downstream, the content of nitrogen and phosphorus in water and soil total nitrogen decreased first and then increased, while the content of nitrogen and phosphorus in the plant, soil nitrate nitrogen, total and available phosphorus gradually increased. There existed an obvious agricultural nitrogen input in the downstream. (2) The total nitrogen content in water was significantly positively related to the nitrogen content in different vegetative organs of plant (P<0.01). Total phosphorus content in water was significantly positively related to soil total and available phosphorus content (P<0.001), and both soil total and available phosphorus content were significantly negatively related to altitude (P<0.001). (3) The content of nitrogen and phosphorus in riparian water were affected by the content of soil nitrogen and phosphorus, plant nitrogen and phosphorus and topography, and among them, soil nitrogen and phosphorus were the dominant factors. The permutation test of available phosphorus at soil depth of 20-40 cm, available phosphorus at 0-20 cm, total phosphorus at 20-40 cm, total phosphorus at 0-20 cm and nitrate nitrogen at 0-20 cm were all significant (P<0.05), with the variation interpretation rate of 25.11%, 21.71%, 11.14%, 8.13% and 3.05%, respectively. The river section had an impact on the content of nitrogen and phosphorus in the water, soil and plants in the riparian zone. From upstream to downstream, nitrogen and phosphorus gradually accumulated, but the difference decreased. Nitrogen and phosphorus in water, soil and plants had a certain correlation with each other, and were also affected by altitude, slope and aspect. Cultivated land was the main cause of agricultural non-point source pollution in the lower reaches of the river basin. It was necessary to strengthen the ability of plant protection and soil conservation in the middle and lower reaches, and to optimize the land use pattern in the riparian zone, so as to provide a basis for agricultural non-point source pollution control in small watersheds in the Three Gorges Reservoir area.