Molybdenite has been established as a robust mineral for Re-Os isotope dating. However, higher-precision Re-Os molybdenite dating is necessary to accurately determine the absolute timing of metal mineralization and duration of ore-forming hydrothermal systems. To improve the precision and accuracy of molybdenite Re-Os dating, molybdenite from the Longmendian deposit—with its old age, heterogeneous distribution of Re, compression deformation, and complex polytypes—serves as a reference for enhancing the precision of in-situ Re-Os dating or grain-scale sampling during solution Re-Os isotope dating of molybdenite. High-resolution scanning transmission electron microscopy (TEM) analysis demonstrates that Re, Os, Pb, Bi, Cu, and Fe are incorporated into the molybdenite crystal through isomorphic substitution for Mo. Electron probe analysis shows that a single molybdenite grain exhibits heterogeneous textures consisting of Re-rich (∼0.29–0.82 wt%) and Re-poor (<0.29 wt%) domains. Some molybdenite grains have undergone compression deformation. Rhenium can be enriched in either the deformed or the undeformed domains of molybdenite grains. Compression deformation in some grains induces delamination cracks in Re-rich domains, facilitating ore-forming fluid infiltration and leading to an inhomogeneous distribution of Re and other elements in molybdenite grains. Re-rich domain in molybdenite is enriched in other metals, including Fe, Co, Zn, Pb, and Bi, due to the overprint of the hydrothermal fluids with a lower temperature and a relatively high oxygen fugacity, leading to the formation of heterogeneous molybdenite. Micro-X-ray diffraction (μXRD) and TEM analyses have revealed that both the Re-rich and Re-poor domains belong to the 2H₁ polytype, indicating that Re concentration and distribution are not directly related to the polytype of molybdenite. The Re-poor and deformed domain of molybdenite shows the coexistence of 2H₁ and 3R polytypes (in a ratio of 9:1), suggesting that compression deformation led to polytype transformation. Therefore, the diverse characteristics of molybdenite in the Longmendian deposit present challenges for obtaining primary Re-Os age information. Nondestructive pre-characterization of molybdenite is essential before dating to ensure age homogeneity. Molybdenite samples with an undeformed and uniform distribution of elements (Re) within molybdenite grains are suitable candidates for analysis. Our findings collectively offer strategies to enhance precision while advancing the understanding of elemental and isotopic geochemical behavior in the contexts of metamorphism, deformation, and fluid flow environments.