Bayan Obo ore deposit is the world’s largest rare-earth element (REE) resource, the second largest niobium (Nb) resource, and also a significant iron (Fe) resource in China. Evaluating resource potential for the deposit has become a focus of global interest. Rock-physical properties bridge geophysical exploration and geologic modeling; variation in these parameters is necessary for successful geophysical application. REE, Nb, iron, and potassium are mainly hosted in dolomite and slate of the Bayan Obo Group, and REE mineralization is genetically associated with carbonatite. Three physical properties (resistivity, polarizability, and magnetic susceptibility [MS]) of iron ore, slate, dolomite, and carbonatite dike outcrop samples at Bayan Obo are measured and statistically analyzed using 3D reconstruction, 1D/2D/3D kernel density estimation, scatterplot matrix, 3D histogram, and Pearson- and maximum information coefficient-based correlation analysis. It is evident that iron ore, iron-mineralized fine-grained dolomite, and iron-mineralized slate are mainly of low resistivity, and iron ore and iron-mineralized fine-grained dolomite have high MS. MS favorably distinguishes iron ore from slate; MS and resistivity distinguish between iron-mineralized fine-grained dolomite and carbonatite dikes. The physical properties and whole-rock geochemistry (major and trace elements) jointly demonstrate that MS of iron ore, slate, and dolomite is positively correlated with TFe2O3 content, polarizability is correlated with TFe2O3, SiO2 content is correlated with K2O, and resistivity is correlated with MS and polarizability, respectively. Resistivity of iron ore and dolomite is negatively correlated with TFe2O3 content. Resistivity of iron ore is negatively correlated with TFe2O3, total REE (), and Nb, respectively, and correlated with thorium. The methods used have intuitive visual expression and reflect the characteristics of the physical properties and their correlation with the mineralogical composition. The results will be beneficial for determining the geometry of ore-hosting rock masses and providing crucial evidence for the resource evaluation.