The location of the Continent–ocean boundary (COB) between the Palawan continent block (PCB) and the central oceanic basin remains controversial. There are more than 100 km difference among the scholars' view about the specific positions of the COB. To obtain a more reasonable location of the COB in the PCB, a comprehensive interpretation was conducted based on new shipborne geophysical data, including bathymetry, gravity, magnetic and reflection seismic data. In particular, upward continuation was applied to the new stern-towing magnetic data, and analytical signal analysis (ASA) processing was adopted for the total field magnetic anomalies, including both the public and stern-towing magnetic data. The most reasonable COB of PCB is just identified with the geophysical data based on the comprehensive structures' anomalies, such as the foot of massif slope and the magmatic volcanoes in topographic data, and the gentle gradient of the free-air and Bouguer gravity anomalies, and the clear dividing boundary in magnetic ASA sharp anomaly, and the seismic profiles structure's display in the Continent–ocean transition (COT). Meanwhile, structural modeling along the seismic profiles are used to constrained the identification. The refined convex–concave's COB is distributed at the seaward limit of the continental crust along the foot of northwest Palawan slope with a hyper-extended thinner crust, seaward-dipping listric faults, and is reasonably located between the extensive thinned continental crust and expansive subducting oceanic crust.