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The Okinawa Trough (OT) is characterized by high heat flow anomalies up to 10,000 mW/m2 (especially in the middle area), which is rarely seen in heat flow research all over the world. The genesis of the high heat flow anomaly is probably related to mantle upwelling. However, the deep genesis is yet to be studied. We used heat flow values collected from the Global Heat Flow Database to calibrate the locations of high heat flow anomalies. Gravity data were used to calculate the residual geoid and interlayer geoid anomalies, which can help in characterizing the morphology of mantle upwelling beneath the OT. Earthquake hypocenter distribution maps were presented to show the position of the Philippine Sea Plate beneath the OT. According to P-wave tomography profile and previous research, we discussed the deep genesis of the high heat flow anomaly and proposed a preliminary model to explain the process. We suggest that the deep mantle upwelling, probably from a depth of −1200 km, enters the upper mantle through the front of the subducted Pacific plate. The deep mantle upwelling converges with the molten mantle flow caused by the fluid from the dehydration of the Pacific Plate and the Philippine Sea Plate. Two mantle upwelling branches were revealed to feed the southern OT (SOT) and Changbai Volcano, and the mantle upwelling under the middle OT (MOT) was the second branch from the mantle upwelling branch under the SOT. The MOT should be more influenced by mantle upwelling from deep sources with extremely high temperatures. • Deep mantle upwelling enters the upper mantle through the front of the subducted Pacific plate. • Two mantle upwelling branches from deep source were revealed to feed the Okinawa Trough and Changbai Volcano. • The genesis of the high heat flow anomaly in the middle Okinawa Trough is probably related to deep mantle upwelling. [ABSTRACT FROM AUTHOR]