The invention provides a carbonatite pore structure characterization method based on rock classification and multi-scale digital cores. The method comprises the following steps: firstly, obtaining core images with different resolutions through a CT scanning technology; then, carrying out binary segmentation on the obtained digital cores, and combining the optimized digital cores with different resolutions together, thereby obtaining multi-scale digital cores; evaluating pore structure parameters of the digital cores, and comparing the pore structure parameters with data measured by experiments; and finally, carrying out regional division on the obtained multi-scale digital cores based on the rock stratification, pore structure and the like, then carrying out property classification on the regions, summarizing the classification results, and filling to regions with same properties. According to the invention, the digital cores with different scales are combined, so that the physical properties of mediums can be characterized, and the requirements for resolutions can be met; and meanwhile, the obtained multi-scale digital cores are subjected to rock classification. The method can greatly reduce the analytical calculation difficulty so as to lay a foundation for processing more complicated cores with stronger non-homogeneity.