Coastal stratification is traditionally considered the primary physical driver of hypoxia by suppressing vertical mixing and dissolved oxygen (DO) ventilation. However, this classical paradigm often fails in highly dynamic estuaries. Using a validated hydrodynamic-biogeochemical model, we reconstructed summer hypoxia in the Pearl River Estuary (PRE) to investigate the physical mechanisms controlling hotspots in the western (WHZ) and eastern (EHZ) shelf regions. A DO budget analysis reveals that, despite significantly stronger stratification, WHZ exhibits a vertical diffusive DO flux that is twice that of EHZ, making it the overwhelmingly dominant term in bottom physical DO supply. This paradox is driven by tidal straining: in WHZ, intense negative tidal straining (<- 1.5 × 10- 4 psu2 s- 1) disrupts stratification and enhances DO diffusion during the late flood phase, even under low shear stress (<0.1 Pa). In contrast, weak tidal straining in the EHZ leaves DO diffusion governed almost entirely by bottom shear stress. Furthermore, in the EHZ, mixing requires nearly a full tidal cycle; by contrast, tidal straining-induced bottom mixing in the WHZ efficiently penetrates the entire water column within half a tidal cycle, making bottom DO dynamics in WHZ strongly tied to stratification fluctuations. This study provides a physical mechanism that explains the bias in the traditional stratification-controlled DO pattern, thereby improving our ability to manage hypoxia in highly dynamic coastal systems.