Dissolved organic matter (DOM) play important roles in the global carbon cycle and aquatic ecosystem health. Estuaries are critical zones connecting the land and the ocean in which fluvial DOM experience dispersion, transformation, degradation, deposition, etc. Yellow River (YR) is the second largest river in China in terms of river length. The water-sediment regulation scheme (WSRS) was implemented in YR since 2002 and around half of the annual sediment and a quarter of the annual water were poured into the estuary in around 20 days. Meanwhile, huge amounts of DOM were discharged into the Yellow River estuary (YRE) rapidly, but it is unclear about their processes and fates in YRE and adjacent seas. This study aims to investigate the molecular and spectrum compositions of DOM and its associated transformation mechanisms around the YRE and its adjacent sea before (from June 8 to 12, 2022) and after (from July 18 to 22, 2022) the WSRS. Relatively higher recalcitrant and terrestrial-derived DOM were found with higher aromaticity and humification degree after WSRS, by bulk geochemical techniques (DOC and δ13C), optical spectroscopy (UV-vis and EEM-PARAFAC analysis) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) techniques. High levels of less photodegraded DOM were found in the estuarine region after WSRS, due to the rapidly pouring huge amount of fresh water and sediment into YRE. Along with the YR plume and coastal current, DOM was transported from the YRE to Laizhou Bay to the south, and arriving at Bohai Strait to the east. Significant decreases in relative intensity and numbers of sulphur-containing compounds in DOM were observed after WSRS. This might be due to the flocculation in the estuarine region and settling of DOM as a result of the high sediment content in the water column. Overall, this research provides valuable insights into the estuary DOM variations induced by the intensive dam-orientated regulation in a short term.