AbstractOne year long, full‐depth velocity measurements were used to examine the spatial structure and temporal variability of the zonal flow in the Luzon Strait (LSZF). The observation revealed a renewed mean flow structure: in the upper (<500 m) and deep (>2000 m) layers, the LSZF was mostly westward; in the intermediate layer (500–2000 m), it was dominated by an eastward flow in the south but a westward flow in the north. The volume transport across the observed section between 19.8°N and 21.2°N exhibited strong seasonal and intraseasonal variability. On the seasonal time scale, the upper‐layer transport showed a clear annual cycle, strongest in January and weakest in June; the intermediate‐layer transport also showed a semiannual cycle, attaining its peaks (troughs) in January and June (April and October). On the intraseasonal time scale, both the upper‐layer and intermediate‐layer transports showed significant energy peaks at about 60 and 10–30 days. Further analysis indicated that the ∼60 day variability might be attributed to the impinging mesoscale eddies from the Pacific, while the 10–30 day variability appeared to obtain its energy from local intraseasonal wind forcing and baroclinic instability of the background current. The 10–100 day upper‐layer and intermediate‐layer transport variabilities were highly anticorrelated, suggesting a baroclinic nature of the intraseasonal variabilities of the LSZF.