Abstract: Reef islands have recently become one of the hot interests in international geoscientific researches. Recent progress indicates that the internal structure of reef island is the key to some scientific issues, such as deep-sea geological evolution, paleo-environmental and paleo-climatic changes and to some engineering problems, for example, the construction of man-made reefs and islands. The Yongle Atoll in the Xisha Islands of the South China Sea, which has experienced the geological evolution as part of the South China Sea and become famous because of the deepest Blue Hole in the world, is a key area for marine scientific research in China. However, the internal structure of the islands is not clear at present due to lack of detecting facilities and imaging methods. Based on the collected high- resolution seismic data with 3.125m trace distance from the Yongle Atoll, this paper revealed for the first time the fine internal structure of the reef islands of the Yongle Atoll with high-precision seismic images by enhancing the signal-to-noise ratio, resolution and imaging accuracy of the seismic data via improvement of seismic data analysis, seismic data processing process and seismic imaging methods. The output indicates that the seismic data processing procedures promoted by this paper has advantages in the migration and reorientation of the seabed reef's diffraction wave, working out clearer shallow structures inside the reef, and acquiring the in-phase axis of seismic reflection from deep water. Our study proves that it is a suitable and effective method for seismic data acquisition and processing in the area of reef islands as such in the South China Sea of China.