Heat flow data (664 measurements) in the Okinawa Trough and adjacent areas are edited and analysed in this study. The distribution of heat flow in the study area is obviously correlated with tectonic zones. The heat flow is extremely high and variable in the back‐arc basin and extremely low in the trench. A 2D transient heat conduction‐advection model is used to test and determine the thermal structure and evolution of the Okinawa Trough under the heat flow distribution constraint. The results show that (a) high sedimentation rates can reduce heat flow by 30–35%; lower heat flow in the southern than in the central‐northern Okinawa Trough might be caused by the thick sediment covering due to the Taiwan orogenic uplift. (b) Heat flow can be enhanced dramatically by mantle upwelling, but magma intrusion accompanied by ascending fluid is necessary for the extremely high heat flow along the central Okinawa Trough axis. A magma intrusion age of 0.5 Ma, an intrusion depth of 1 km, and a fluid flow speed in the magma of 9 cm/year are the best fit parameters for the central Okinawa Trough. (c) Given the distribution of heat flow, we suggest that the evolutionary model differs between the central‐northern and the southern Okinawa Trough. The rifting in the central‐northern Okinawa Trough began at 10 Ma with a mean rate of 0.4 cm/a, while the rifting in the south Okinawa Trough started at 6 Ma with a higher rate of 0.6 cm/a. (d) A double magma chamber may exist underneath the axis of the Okinawa Trough at depths of 10 and 24–30 km beneath the seafloor. The temperatures and pressures at these depths support the existence of partial melting, which became the primary basis for maintaining the extremely high heat flow currently observed in the Okinawa Trough.