The Mufushan Complex (MFSC) is a significant rare metal mineralized in the central China district and is renowned for its marked economic value of rare metal deposits. While the main rare metal mineralization (RMM) stage in the MFSC relates to the magmatic event of two-mica monzogranite, the mineralization event related to biotite monzogranite remains unknown. To fill this gap, this study focuses on porphyritic biotite monzogranite and adjacent Be-rich pegmatite samples obtained from Changqing Pegmatite No. 1, which is situated in the southeastern part of the MFSC. We subjected these samples to zircon U–Pb dating and Hf isotope analysis using laser ablation inductively coupled plasma mass spectrometry (LA–ICP–MS) and utilized an electron probe X-ray microanalyzer (EPMA) and LA–ICP–MS to examine the major and trace elements present in the muscovite samples. Our findings revealed precise chronological data for the geological history of Changqing, pinpointing the intrusion age of biotite monzogranite to 145.8 ± 1.1 Ma and the crystallization age of Be-rich pegmatite to 144.9 ± 1.1 Ma, firmly situating these events within the Late Jurassic to Early Cretaceous epoch. Regarding isotopic composition, zircon εHf (t) for granite ranged from −9.29 to −5.09, and their corresponding TDM2 ranged from 1788 to 1520 Ma. Similarly, zircon εHf (t) for pegmatite ranged from −7.89 to −5.47, and their corresponding TDM2 ranged from 1699 to 1544 Ma. These isotopic signatures strongly indicate a shared origin for the initial magma of granite and pegmatite. The partial melting of the thick Lengjiaxi Group tasedimentary strata serves as a material source for RMM. The transition from granite to pegmatite exhibits remarkable constancy in the primary components of muscovite. By examining its geochemical attributes, we observed synchronous decreases in FeO, MgO, SiO2, MnO, Be, Rb, and Cs, coupled with synchronous increases in Nb and Ta contents, along with Ta/Nb values. These findings strongly imply that the Changqing biotite monzogranite and Be-rich pegmatite originate from the continuous differentiation and evolution of a common magmatic source, establishing a clear genetic relationship between them. The MFSC has its origins in three distinct stages of magmatic activity and RMM spanning from 160 Ma to 120 Ma. Considering the distribution patterns of similar pegmatite veins, the metallogenic potential observed during the biotite granite stage may serve as an external indicator of marked mineralization within large batholiths.