Abstract Understanding how dissolved organic matter (DOM) responds to extreme climate events is critical for predicting carbon cycle feedbacks and ecosystem responses under climate change. However, the biogeochemical consequences of such events in large river‐influenced estuarine and coastal areas remain poorly understood. This study investigated seasonal variations in DOM composition off the Changjiang Estuary—a region strongly influenced by terrestrial inputs—during an extremely dry year. Field surveys were conducted in March, July, and October, using amino acid biomarkers and Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS) to characterize DOM composition. Seasonal analysis revealed a higher contribution of terrestrial (highly degraded) DOM in March, whereas marine (fresh, phytoplankton‐derived) DOM was more prominent in July, and intensified microbial processing of DOM in October. These trends were supported by the degradation index (2.4 ± 0.4, 3.8 ± 0.6, 3.1 ± 0.5) and the carboxyl‐rich alicyclic molecules abundance (58.3 ± 1.0%, 57.9 ± 1.8%, 61.8 ± 1.2%) in March, July, and October. Seaward transport showed a significant loss of compounds containing three or five oxygen atoms and one sulfur atom (O 3 S + O 5 S), indicating enhanced removal of terrestrial light‐sensitive DOM components. The abnormally low refractory fraction and high labile fraction in July suggested a rapid DOM turnover potentially induced by climate anomalies. These findings indicate that extreme drought conditions can significantly alter the DOM cycle and accelerate organic carbon turnover in estuarine and coastal areas. Our findings highlight the importance of incorporating episodic extreme climate events into future assessments of ocean carbon dynamics.