Abstract: Due to the dual influence of shallow low velocity anomalies and T50 high-speed reef limestone layers, traditional velocity modeling method is difficult to accurately characterize shallow anomalies, reef limestone, and small-scale geological bodies in the M area of the South China Sea, resulting in heavy distortion of underlying structural imaging. The low amplitude structures shown on seismic profiles are difficult to determine true or false, posing significant risks to oil and gas exploration. Compared to traditional velocity modeling techniques, full waveform inversion (FWI) is more capable to update velocity models, to comprehensively use seismic rotation and reflection wave information, and to establish high-precision velocity models. By introducing the FWI technology, we designed acquisition parameters through forward modeling, obtained seismic data that can meet the application of FWI technology, studied the full waveform velocity inversion methods for the target area, and formed a high-precision velocity modeling technology process for reef limestone areas. First, the initial velocity was obtained through high-precision grid tomography. Secondly, the shallow velocity model and the mid deep low-frequency velocity model were updated using the rotational wave FWI. The high-frequency component of the velocity model was updated using the reflected wave FWI. Ultimately, the accuracy of velocity characterization for shallow anomalous bodies, reef limestone, and underlying strata was improved, and low amplitude structural imaging artifacts were eliminated. This study provided a strong support for target evaluation in the M area of the South China Sea and a good reference for the development of solutions to similar problems in other sea areas.