Seasonal hypoxia–reoxygenation exposes coastal dissolved organic matter (DOM) to recurrent redox oscillations, but the molecular and microbial responses after reoxygenation remain poorly constrained. Four cruises were conducted across the East China Sea shelf in 2023, covering pre‑hypoxic, hypoxic, and reoxygenated stages. Optical and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) characterization, 16S rRNA gene sequencing, and bacteria–molecule network analysis were combined to examine stage-dependent DOM restructuring and microbial coupling. After excluding major physical effects, apparent oxygen utilization (AOU)-associated formulae accounted for only 3.10–5.24% of retained formulae but exhibited pronounced seasonal restructuring. Hypoxia favored accumulation of high-O/C, Sulfur-rich, high-mass molecules and enhanced oxidation and sulfurization transformation. Reoxygenation shifted net accumulation toward highly unsaturated carboxyl-rich alicyclic (CRAM)-like molecules, with increased nitrogen incorporation and renewed degradation/mineralization. This accumulation of refractory‑like compounds may enhance the preservation potential of DOM and its offshore export. The persistence of hypoxia‑related bacterial groups and the maintenance of elevated network connectivity indicate that “post-hypoxia sequelae” in DOM composition and bacteria–DOM interactions can persist for approximately one month after oxygen recovery.