The southern part of the Kyushu-Palau Ridge (KPR) is located at the conjunction of the West Philippine Basin, the Parece Vela Basin, the Palau Basin, and the Caroline Basin. This area has extremely complex structures and is critical for the research on the tectonic evolution of marginal seas in the Western Pacific Ocean. However, only few studies have been completed on the southern part, and the geophysical fields and deep structures in this part are not well understood. Given this, this study finely depicts the characteristics of the gravity and magnetic anomalies and extracts information on deep structures in the southern part of the KPR based on the gravity and magnetic data obtained from the 11th expedition of the deep-sea geological survey of the Western Pacific Ocean conducted by the Guangzhou Marine Geological Survey, China Geological Survey using the R/V Haiyangdizhi 6. Furthermore, with the data collected on the water depth, sediment thickness, and multichannel seismic transects as constraints, a 3D density model and Moho depths of the study area were obtained using 3D density inversion. The results are as follows. (1) The gravity and magnetic anomalies in the study area show distinct zoning and segmentation. In detail, the gravity and magnetic anomalies to the south of 11°N of the KPR transition from high-amplitude continuous linear positive anomalies into low-amplitude intermittent linear positive anomalies. In contrast, the gravity and magnetic anomalies to the north of 11°N of the KPR are discontinuous and show alternating positive and negative anomalies. These anomalies can be divided into four sections, of which the separation points correspond well to the locations of deep faults, thus, revealing different field-source attributes and tectonic genesis of the KPR. (2) The Moho depth in the basins in the study area is 6–12 km. The Moho depth in the southern part of KPR show segmentation. Specifically, the depth is 10?12 km to the north of 11°N, 12?14 km from 9.5°N to 11°N, 14–16 km from 8.5°N to 9.5°N, and 16?25 km in the Palau Islands. (3) The KPR is a remnant intra-oceanic arc with the oceanic-crust basement.which shows noticeably discontinuous from north to south in geological structure and is intersected by NEE-trending lithospheric-scale deep faults. With large and deep faults F3 and F1 (the Mindanao fault) as boundaries overall, the southern part of the KPR can be divided into three zones. In detail, the portion to the south of 8.5°N (F3) is a tectonically active zone, the KPR portion between 8.5°N and 11°N is a tectonically active transition zone, and the portion to the north of 11°N is a tectonically inactive zone. (4) The oceanic crust in the KPR is slightly thicker than that in the basins on both sides of the ridge, and it is inferred that the KPR formed from the thickening of the oceanic crust induced by the upwelling of deep magma in the process of rifting of remnant arcs during the Middle Oligocene. In addition, it is inferred that the thick oceanic crust under the Palau Islands is related to the constant upwelling of deep magma induced by the continuous northwestward subduction of the Caroline Plate toward the Palau Trench since the Late Oligocene. This study provides a scientific basis for systematically understanding the crustal attributes, deep structures, and evolution of the KPR.