In order to understand the source and spatial distribution regularities of PAEs and the main environmental factors affecting their distribution in the tributary of the Three Gorges Reservoir, Five sections in Yulin River, the first level tributa at the end of the Three Gorges Reservoir, were selected: the Estuary, the backwater area (Paihua, Shujia, Meixi) and the upsteam inflow area (Donghe), which was not affected by the operation of the Three Gorges Reservoir, to conduct an in-situ investigation on PAEs. Based on Pearson correlation analysis and principal component analysis, the sources of six PAEs in Yulin River and the relationship between the main PAEs and environmental factors were identified. The results of in-situ investigations of 6 kinds of PAEs (DEP, DMP, DBP, BBP, DEHP and DnOP, according to US EPA) in five monitoring section of the Yulin River revealed that the total concentration of PAEs was in the range of 0.42~0.77 μg/L. The average total concentrations of PAEs in the five monitoring sections were: Estuary (0.771 μg/L) > Paihua (0.638 μg/L) > Meixi (0.613 μg/L) > Donghe (0.566 μg/L) > Shujia (0.421 μg/L), with DMP, DBP and DEHP being the primary monomers. Based on the correlation analysis and principal component analysis, it was found that there was a significant positive correlation between DBP and DEHP, which may be related to industrial and agricultural production activities and the “three wastes” generated in the process. The moderate correlation between DMP and DEP indicated that these pollutants may be attributed from the anthropogenic activities of local residents.