Abstract The deep western boundary current (DWBC) was studied based on a full-depth mooring east of Luzon Island in the Northern Philippine Sea deep basin during the period from January 2018 to May 2020. On average, the DWBC in the Philippine Sea flows southward with a velocity of approximately 1.18 cm s−1 at a depth of 3050 m. Significant intraseasonal and seasonal variations of the DWBC are identified. The intraseasonal variations have multiple spectral peaks in the range of 30–200 days, with the most obvious peak at approximately 120 days. On the seasonal time scale, the DWBC intensifies in summer/autumn and weakens in winter/spring, corresponding well with the seasonal variation of the ocean bottom pressure (OBP) from the Gravity Recovery and Climate Experiment. Both intraseasonal and seasonal variations have no significant correlation with the temporal variations in the upper and middle layers but have a certain correlation with transport through the Yap–Mariana Junction (YMJ). A set of experiments based on an inverted-reduced-gravity model and the OBP data reveal that the temporal variations originating from the YMJ could propagate counterclockwise along the boundary of the deep basin to the western boundary of the deep Philippine Sea, dominating the temporal variations of DWBC.