The Huangliangou Nb-Ta-Be deposit in the Baoshan Block of western Yunnan hosts two distinct generations of columbite–tantalite group minerals (CGMs) and tapiolite, which record the evolution of a highly fractionated rare metal pegmatite. To investigate the relationship between Huangliangou pegmatite differentiation and Nb-Ta mineralization, we conducted an integrated study combining petrography with mineral chemistry and geochronology. Electron probe microanalysis (EPMA) was used to determine the compositions of two CGMs and tapiolite. LA-ICP-MS U-Pb dating of these Nb-Ta oxides yields weighted mean ages of 60.25 ± 0.75 Ma for CGM-1 and 59.4 ± 1.1 Ma for CGM-2, indicating their synchronous formation in the early Paleocene. LA-ICP-MS trace element analysis of muscovite reveals a trend of decreasing Nb/Ta and K/Rb ratios with increasing Cs content from two-mica to garnet-bearing pegmatites. This chemical evolution in muscovite parallels the mineralogical transition from magmatic CGM-1 to metasomatic CGM-2 and tapiolite, confirming that late-stage hydrothermal fluids were characterized by volatile enrichment and Ta accumulation. The textural and chemical evolution reflects a late-stage, fluid-assisted autometasomatism within a highly fractionated melt. These results identify the northern garnet-bearing pegmatite dikes as a high-priority target for Ta exploration and provide a chrono-lithological framework for prospecting Paleocene pegmatite-type Nb-Ta deposits in western Yunnan and comparable Tethyan settings.