The Sulawesi Sea and Sulawesi Island are located in the western Pacific area where volcanic activity, plate subduction, and seismic activity are very active. The Sulawesi basin formed during the Middle Eocene-Late Eocene and nearly half of the Eocene oceanic crust has subducted below the North Sulawesi Trench. The Sulawesi Island was spliced and finalized in the Early Pliocene-Pleistocene during volcanic activity and is recently very active. This area is an optimal location to study volcanic geothermal conditions and subduction initiation mechanisms in the southern part of the western Pacific plate margin, which are important in geothermal and geodynamic research. In this study, we combined 133 heat flow data with gravity and magnetic data to calculate the Moho structure and Curie point depth of the Sulawesi Sea and periphery of the Sulawesi Island, and analyze the distribution characteristics of the geothermal gradient and thermal conductivity. The results show that the average depths of the Moho and Curie surfaces in this area are 18.4 and 14.3 km, respectively, which is consistent with the crustal velocity layer structure in the Sulawesi Basin previously determined by seismic refraction. The average geothermal gradient is 4.96°C (100 m)−1. The oceanic area shows a high geothermal gradient and low thermal conductivity, whereas the land area shows a low geothermal gradient and high thermal conductivity, both of which are consistent with statistical results of the geothermal gradient at the measured heat flow points. The highest geothermal gradient zone occurs in the transition zone from the Sulawesi Sea to Sulawesi Island, corresponding to the spreading ridge of the southward-moving Sulawesi Basin. Comprehensive gravity, magnetic, and geothermal studies have shown a high crustal geothermal gradient in the study area, which is conducive to the subduction initiation. The northern part of the Palu-koro fault on the western side of Sulawesi is likely the location where subduction initiation is occurring. During the process of moving northwest, the northern and eastern branches of Sulawesi Island have different speeds; the former is slow and the latter is fast. These branches also show different deep tectonic dynamic directions; the northern branch tilts north-up and the eastern branch tilts north-down.