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 severe distortion of underlying structural imaging. The low amplitude structures displayed on seismic profiles are difficult to distinguish between true and false, posing significant risks to oil and gas exploration. Compared to traditional velocity modeling techniques, Full Waveform Inversion has stronger ability to update velocity models and can comprehensively utilize seismic rotation and reflection wave information to establish high-precision velocity models. This article is driven by FWI technology, and designs acquisition parameters through forward modeling to obtain seismic data that can meet the application of FWI technology. It also conducts research on full waveform velocity inversion methods for the target area, forming a high-precision velocity modeling technology process for reef limestone areas. Firstly, 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, eliminating low amplitude structural imaging artifacts. This provides strong support for target evaluation in the M area of the South China Sea and has good reference significance for the development of solutions to similar problems in other sea area.