Shallow sea underwater topography plays an important role in the development of islands and reefs. The Qilianyu Islands, located in Xisha, South China Sea, are a key area for the development and utilization of the South China Sea. Compared with traditional underwater topography detection methods, synthetic aperture radar (SAR) has the advantages of low cost, short time consumption, and the large-scale detection of shallow water topography. The GF-3 satellite is the first SAR satellite launched by China, and its ability to probe shallow sea topography has never been assessed. To detect the underwater topography of the Qilianyu Islands and test the application of GF-3 SAR data in shallow sea underwater topography detection, this paper implements the SAR shallow sea underwater topography detection model, the tidal information corresponding to the imaging time of the SAR image, and six GF-3 SAR images to detect the underwater topography of the Qilianyu island and reefs. The detection results have been analyzed from different imaging times, different water depths and different polarization modes, and the first four SAR images show promising detection results. The average absolute error (MAE) and average relative error (MRE) of the results are 1.5 m and 14.33%, respectively, which demonstrates that GF-3 SAR images have an impressive performance in underwater topography detection of South China Sea island reefs.