Because the 2D (two-dimensional) characterization analysis of mineral dissemination characteristics requires complex sample preparation, destroys the sample structure, and produces stereological errors, a new method for analyzing mineral dissemination characteristics in the ore in situ, non-destructively and stereoscopically, is required. The research object in this paper is a medium–low grade calcareous-magnesium phosphate ore in Guizhou, and XMT (X-ray microtomography) and BPMA (BGRIMM Process Mineralogy Analysis) are used to conduct a comparative study of 3D (three-dimensional) and 2D analysis of mineral dissemination characteristics. The results of grain size analysis show that fluorapatite and gangue minerals belong to equal-grain dissemination, with very little fine particle content. The results of 2D analysis are finer than those of 3D analysis, but 3D non-destructive analysis produces more accurate results. In addition to particle size analysis, the binding relationship between minerals analysis results show that, when compared to the 2D distribution of minerals, 3D visualization can more intuitively and stereoscopically observe the distribution of minerals inside the ore and the intergrowth relationship between minerals. Through comparative study, it can be seen that the application of 3D visualization has developed a new method for the study of mineral dissemination characteristics, which makes up for the shortcomings of 2D analysis.