Submarine sinkholes are unique and important geomorphological features with a typical cavity structure that are of great scientific value. Submarine sinkholes were discovered for the first time in the isolated Ganquan carbonate platform on the Xisha Islands, the northwestern South China Sea. Based on high-resolution multibeam bathymetric data and seismic profile data, we identified 37 submarine sinkholes at water depths ranging from 550 to 1267 m. They are subcircular to circular negative-relief features, and most of them are V- or compound V-shaped in the cross-section. Their average diameters range from 57 to 667 m, and the depth of the depression ranges from 2.5 to 241 m. By comparing submarine sinkholes in the Ganquan platform with those in other carbonate platforms worldwide, we can infer that the Ganquan platform submarine sinkholes are the largest sinkholes developed on an isolated carbonate platform. Remotely operated vehicle (ROV) “Haima 2” images revealed that the inner walls of submarine sinkholes are characterized by stalactite-like structures, possible dikes, flow marks, and corroded holes, which are typical karstic landscape features. The temperature within submarine sinkholes is 2 °C higher than that of the open ocean at the same water depth. Based on the results of the shallow formation profile and multichannel seismic profiles, we propose that the submarine sinkholes in the Ganquan platform probably formed via the dissolution of the carbonate platform via acidic hydrothermal fluids that originated from magmatic activity and migrated along faults.