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The Maluku Channel is a major opening of the eastern Indonesian Seas to the western Pacific Ocean, the upper-ocean currents of which have rarely been observed historically. During December 2012–November 2016, long time series of the upper Maluku Channel transport are measured successfully for the first time using subsurface oceanic moorings. The measurements show significant intraseasonal-to-interannual variability of over 14 Sv (1 Sv ≡ 106 m3 s−1) in the upper 300 m or so, with a mean transport of 1.04–1.31 Sv northward and a significant southward interannual change of over 3.5 Sv in the spring of 2014. Coincident with the interannual transport change is the Mindanao Current, choked at the entrance of the Indonesian Seas, which is significantly different from its climatological retroflection in fall–winter. A high-resolution numerical simulation suggests that the variations of the Maluku Channel currents are associated with the shifting of the Mindanao Current retroflection. It is suggested that the shifting of the Mindanao Current outside the Sulawesi Sea in the spring of 2014 elevates the sea level at the entrance of the Indonesian Seas, which drives the anomalous transport through the Maluku Channel. The results suggest the importance of the western boundary current nonlinearity in driving the transport variability of the Indonesian Throughflow.