The South-to-North Water Diversion East Project (SNWDP-E) is an effective way to realize the optimal allocation of water resources in China. The North Dasha River (NDR) is the reverse recharge section that receives water from the Yufu River to the Wohushan Reservoir transfer project line in the SNWDP. However, the dissolved organic matter (DOM) evolution mechanism of seasonal water transfer projects on tributary waters has not been fully elucidated. In this paper, the NDR is the main object, and the changes in the composition and distribution of spectral characteristics during the winter water transfer period (WT) as well as during the summer non-water transfer period (NWT) are investigated by parallel factor analysis (PARAFAC). The results showed that the water connectivity caused by water transfer reduces the environmental heterogeneity of waters in the basin, as evidenced by the ammonia nitrogen (NH4+-N) and total phosphorus (TP) in the water body were significantly lower (p<0.05, p<0.01) during the water transfer period than the non-water transfer period. In addition, the fluorescence intensity of DOM was significantly lower in the WT than the NWT (p<0.05) and was mainly composed of humic substances generated from endogenous sources with high stability. While the NWT was disturbed by anthropogenic activities leading to significant differences in DOM composition in different functional areas. Based on the redundancy analysis (RDA) and multiple regression analysis, it was found that the evolution of the protein-like components is dominated by chemical oxygen demand (COD) and NH4+-N factors during the WT. While the NWT is mainly dominated by total nitrogen (TN) and TP factors for the evolution of the humic-like components. This study helps to elucidate the impact of water transfer projects on the trunk basin and contribute to the regulation and management of inter-basin water transfer projects.