Taiwan Strait (TWS) plays a crucial role in material exchange and nutrient budget between the South China Sea and the East China Sea. In this study, we investigate the variability of volume transport in the TWS and its response to tropical Madden–Julian Oscillation (MJO) convection based on the simulated results from a three-dimensional operational numerical model. Validated by the observational data, the model generally reproduced the physical field well. The volume transport in the TWS has strong seasonal cycles as well as higher-frequency variations. Intra-seasonal fluctuations dominate the along-strait currents variability, while secondary and the last signal are seasonal one and inter-annual variability, respectively. Overall, the along-strait wind stress plays a more important role in controlling the variability of volume transport in the TWS than the pressure gradient induced by north-to-south sea level slope. At intra-seasonal time scales, the volume transport in the TWS varies with the movement of the tropical MJO convection from Indian Ocean eastward to the western Pacific Ocean. These oceanic anomalies are related to atmospheric anomalies, with a distinct physical linkage from the tropical atmosphere to the mid-latitude ocean. The tropical MJO deep convection can modify the upper tropospheric heights and generate a wave train pattern that propagates to mid-latitudes. In addition, these anomalous upper tropospheric heights modulate the surface pressure, resulting in a cyclonic anomaly. The upper tropospheric heights anomaly and its corresponding mean sea level pressure anomaly move eastward in the MJO cycle following the migrating MJO heat source in the tropics from phase 2 to 5. Consequently, surface winds change as the cyclonic anomaly moves from central China to the east of Japan, resulting in a northeast volume transport anomaly during MJO phase 2 and 3 and a southwest volume transport anomaly during MJO phase 4 and 5.