Significant short-term fluctuations of the Yellow Sea Warm Current (YSWC) at several days' time scale were observed in the Yellow Sea (YS) during winter of 2006–2007. Observations indicated that the synoptic fluctuations of the YSWC appear to be associated with low-frequency sea level variations. By analyzing direct current measurements, sea level elevations and results from a regional ocean model, this study characterizes the variation of the YSWC at synoptic time scale and examines its connection with propagation of coastal-trapped waves during winter. The model captures the observed short-term fluctuations of the YSWC at several days’ periods and suggests a close relation between coastal-trapped waves and the YSWC variability. The YSWC is intensified (weakened) when the westward sea level-related barotropic pressure gradient is enhanced (diminished) due to the propagation of coastal-trapped waves. Model experiments with idealized periodic surface forcing further identify the important role of the coastal-trapped waves on adjusting the strength of the YSWC. The model results also suggest that the propagation of coastal-trapped waves contribute to the intermittent northwestward intrusion of Cheju Warm Current (CWC) in the frontal region northwest of Cheju. Generation and propagation of the coastal-trapped waves give rise to the westward barotropic pressure gradient in the YS entrance, which periodically pumps the CWC water into the YS interior west of Cheju.