Qiongdongnan Basin is an important research object for deep-water exploration in the South China Sea. The basin was currently less drilled and explored, but it had a wide exploration prospect. Time-depth conversion had been the focus of research in Qiongdongnan Basin. Velocity, as an important bridge of transforming the results of exploration from time to depth, played a decisive role in the exploration of geological structure and design of drill hole. The average velocity changed largely on the horizon in Qiongdongnan Basin and there was a large deviation between seismic velocity and well velocity. According to statistical analysis, it was found that there were three types of deviation between seismic velocity and well velocity.