The invention provides a method for identifying a reef cap, a reef core and a reef base. The method includes steps: respectively obtaining respective seismic reflection structure samples of the reef cap, the reef core and the reef base; performing fusion on a low-frequency interpreting result curve and a high-frequency logging curve to form a high-frequency constrained curve, wherein the high-frequency logging curve has different response ranges of the reef cap, the reef core and the reef base; and performing waveform difference inversion by employing the respective seismic reflection structure samples of the reef cap, the reef core and the reef base, seismic data of a research region and the high-frequency constrained curve to identify the reef cap, the reef core and the reef base. By employing the method, the identification of the reef cap, the reef core and the reef base is accurate and reliable, the resolution is high, the reef cap, the reef core and the reef base of the whole research region can be identified, and the distribution conditions of the reef cap, the reef core and the reef base in the whole research region can be understood.