East Asian dust outbreaks are accompanied by pronounced synoptic circulation anomalies, yet their influence on phytoplankton variability through atmospheric forcing remains poorly understood. Here we investigate the response of chlorophyll-a (Chl-a) to spring dust optical depth (DOD) in the Chinese marginal seas during 2003–2023 using daily anomalies from reanalysis products and a reconstructed Chl-a dataset. We find contrasting Chl-a responses to DOD between the Northern and Southern Chinese marginal seas. The Northern Region exhibits an initial Chl-a suppression followed by a positive anomaly persisting for about one week, while the south shows an immediate positive response that gradually weakens. These distinct patterns are associated with ocean mixed-layer depth (MLD) adjustments driven by dust-related synoptic circulation. Over the northern seas, Mongolian cyclones produce positive air–sea temperature and humidity gradients through anomalous southerly winds, thus reducing upward latent and sensible heat fluxes and promoting net ocean heat gain and initial mixed-layer shoaling before subsequent deepening. In contrast, southern dust events are associated with migrating anticyclones that drive strong northeasterly winds, generating negative air–sea thermal and moisture gradients and intensified upward latent heat flux, thereby promoting net ocean heat loss and mixed-layer deepening. Net surface heat flux exhibit the strongest negative correlation with MLD at a one-day lag in both regions, and surface heat loss-driven mixed-layer deepening generally coincides with elevated Chl-a anomalies. These results highlight synoptic-scale atmospheric forcing and air–sea heat exchange as important physical pathways linking dust variability to short-term Chl-a changes in the Chinese marginal seas.