Temperature is an important factor that affects the stability of a gas hydrate. To investigate the geothermal characteristics in the gas hydrate drilling area, heat flow measurements were performed in the surrounding area of the SH2 well. The measured heat flow was compared with the bottom simulating reflector heat flow, which was calculated by using the depth of the bottom simulating reflector in the seismic data. Combined with the geological background of the Shenhu drilling area, we analyzed the reasons for the differences between the measured heat flow and the bottom simulating reflector heat flow. In addition to analyzing the differences caused by the calculation parameters, we calculated the 3-D topographic effects on the measured heat flow by using the finite element numerical simulation method. The results show that the measured heat flow was seriously affected by the topography and produced a -50-30% error in the study area. After terrain correction of the measured heat flow, we found that the data were greater than the bottom simulating reflector heat flow at almost all sites. Therefore, we considered the impact of fluid activity and calculated the relationship among the thickness of the gas hydrate stability zone, the fluid flux and the heat flow. The results show that when the base of the bottom simulating reflector was at a certain depth, the geothermal gradient increased with the increasing upward migration of the fluid flux. Therefore, when upward fluid migration is present, the measured heat flow in the seafloor sediments is greater than the heat flow in the deep layers. In general, we showed that the influences of the topography and fluid activity are the main factors leading to the inconsistency between the bottom simulating reflector heat flow and the measured heat flow in the Shenhu gas hydrate drilling area.