As a strategic water conservancy project in the lower reaches of the Yangtze River in China, the project has multiple missions such as alleviating the shortage of water resources in Huaibei, improving the ecology of Chaohu Lake and Huaihe River, and promoting the sustainable development of the river basin. Dissolved organic matter (DOM) is an important indicator for assessing the health status of water bodies and tracing pollution sources. Study on its response process to inter-basin water transfers can accurately track the characteristics of water quality changes induced by such transfers, which is of great significance for optimizing ecological scheduling strategies and ensuring water environmental security in the Jiang-huai region. In this study, we selected the Yangtze-Chao section and Yangtze-Huai section in the water diversion project from the Yangtze River to Huaihe River (Anhui section), systematically analysed the source, composition and distribution characteristics of dissolved organic matter (DOM) and its influencing factors in the water diversion project (Anhui section) from the Yangtze River to Huaihe River at the different hydrological periods from December 2023 to June 2024. The results show as follows: (1) the concentration of total nitrogen (TN), ammonia nitrogen and permanganate index (CODMn) in the water bodies during the different hydrological periods showed increasing trends in the dry season, wet season and normal flow season, and their concentrations decreased after water diversion, especially in the Yangtze-Huai section the concentration of TN decreasing from 4.00±1.45 mg/L to 2.06±0.58 mg/L. TP concentration did not change with the spatial and seasonal distributions. DOC concentration showed significant seasonal and spatial variation. During the dry season, the concentrations of DOC in lakes and estuaries were relatively high, while DOC in river section was low. (2) Four DOM fluorescent components were identified, namely marine-derived humus C1, funic acid humic C2, humic acid C3, and tryptophan group proteins C4. DOM was both influenced by autogenic and terrestrial sources. There is no significant seasonal variation in the proportion of autogenic and terrestrial organic matter in the water during different hydrological periods. After water regulation, there is no obvious difference in the spatial distribution characteristics of DOM fluorescence intensity and DOC concentration due to water exchange. (3) TN, CODMn, DO, Chl-a and WT had a significant impact on the composition and concentration of DOM, while the increase of water temperature and DO had a promoting effect on algae growth and degradation of organic matter. The increase of TN concentration led to the eutrophication of water body and the accumulation of DOM. This study evaluated the water environment quality along the Anhui section of the Yangtze-to-Huaihe water diversion project after its initial implementation of water diversion. It reveals the response patterns of DOM in the early stages of inter-basin water transfer and provides a scientific basis for scheduling the water diversion project from a water quality safety perspective.