Dissolved organic matter (DOM), as a precursor of disinfection byproducts and a complexing agent for heavy metals, has significant environmental effects on water quality safety and ecosystem health. This article reviews the sources, environmental effects, and regulatory mechanisms of DOM in reservoirs, outlines the research progress of advanced analytical techniques such as high resolution mass spectrometry and three dimensional fluorescence spectroscopy in revealing the molecular diversity and environmental behavior of DOM, and explores the methodological approaches for accurately predicting the potential for disinfection byproduct formation and carbon sequestration efficiency by integrating multiple analytical techniques with algorithms, such as random forests and neural networks to decipher DOM molecular fingerprints. It has been discovered that DOM in reservoirs serves as both a carbon sink and a carbon source, and its molecular structural characteristics have a significant impact on greenhouse gas emissions and carbon sequestration efficiency. The sources of DOM in reservoirs include terrestrial inputs and endogenous releases, and are regulated by hydrological regulation, redox conditions, and microbial activity. Future work should emphasize interdisciplinary integration and the development of a systematic reservoir DOM database to support the effective implementation of the national “dual carbon” strategy.