The present invention belongs to the field of treatment for data identification and recording carriers, and specifically relates to a method and system for analyzing filling for a karst reservoir based on spectrum decomposition and machine learning, which aims to solve the problems that by adopting the existing petroleum exploration technology, the reservoir with fast lateral change cannot be predicted, and the development characteristics of a carbonate cave type reservoir in a large-scale complex basin cannot be identified. The method comprises: acquiring data of standardized logging curves; obtaining a high-precision 3D seismic amplitude data body by mixed-phase wavelet estimation and maximum posteriori deconvolution and enhancing diffusion filtering. According to the method and the system, the effect of identifying the development characteristics of the carbonate karst cave type reservoir in the large-scale complex basin can be achieved, and the characterization precision is improved.