Micro-X-ray fluorescence (µ-XRF), an increasingly developed spectroscopic technical method, can efficiently search for metallogenic clues in ore deposit research without damaging the sample. In this study, the elemental distribution on the hand specimen and on the microscopic scale of the surface of the bulk uranium ore sample from the Qianjiadian sandstone-hosted uranium deposit in northeast China was investigated using micro-X-ray fluorescence (µ-XRF) instrumentation (Bruker M4 TORNADO PLUS). The elemental distribution of the bulk sample showed the enrichment of typical U-related elements, such as S, P, and Ca, visualizing the mineral vein structure. Furthermore, decimeter-scale samples of the bulk sample contiguous to the mineral vein and surrounding rock were collected by converting the µ-XRF mapping data into matrix sequence data. The surrounding rock proximal to the mineral vein has a depleted Fe content (average cps = 38) compared to the primary surrounding rock (average Fe cps = 68). Interestingly, uranium minerals were related to pyrite (FeS2) in the mineral vein of our bulk sample, probably associated with sulfatereducing bacteria (SRB). This implies that the surrounding rock can produce Fe through pyrite precipitation under biological activity, and U ions carried by ore groundwater or fluid can precipitate through pyrite reduction. Finally, we present a model of element migration between the mineral vein and the surrounding rock in the Qianjiadian deposit. This explains why uranium minerals are usually found as intergrowths around biogenic pyrite. Our research shows that µ-XRF can be an efficient tool for studying ore sample to collect complete chemical data for a better understanding of the metallogenic process.