Abstract: The Okinawa Trough has high but variable mean heat flow values and extensive hydrothermal activities are developed there, especially in the south and north segments of the trough. These geothermal characteristics are closely related to the past and present sedimentation process and fluid activities in the shallow basement aquifers. This paper firstly calculated the background seafloor heat flow values on the basis of Curie Point Depth data, and compared them with the measured data to analyze the features of heat flow anomalies in the Okinawa Trough. Then, we selected a modeling profile along the spreading center and used the thermal modeling method to explore the influences of sedimentation rate and basement fluid activity on the seafloor heat flow. At last, we analyzed and discussed the possible genetic mechanisms of geothermal features. Modeling results indicate that, if extensional processes start at the middle Miocene for the South Okinawa Trough (SOT) and at the late Pleistocene for the Middle Okinawa Trough (MOT) and the North Okinawa Trough (NOT), the present seafloor heat flow would be reduced by 7%~16% for SOT and 4%~12% for MOT with the influence of sediment process; the larger the sedimentation rate is, the greater the effect will be produced. Fluid activities in the basement aquifers brought about the significantly scattered heat flow values, which were reduced above the upward flow and increased above the downward flow. With more influence of upward flow than that of sediment process, some values were increased up to 3 times of background values. On the premise of an equal fluid migration rate for upward flow and downward flow, a sedimentation rate of 25 cm/a and a fluid migration rate of 60~66 cm/a qualify the formation condition of geothermal anomalies in the western SOT. While for the formation of geothermal features nearby Gonggu fracture zone and in the MOT, it requires a migration rate of about 4~6 times or a heat supply (below basement aquifers) of about 2~3 times relative to that of SOT. The latter implies the existence of a magma chamber shallower than 10 km.