The Michang-Bobai belt is a newly recognized W-Mo metallogenic belt in the Guangxi province, SE China. In this paper, we report new U-Pb ages, and petrological, geochemical and Sm-Nd isotopic data for the Youmapo pluton associated with W-Mo mineralization. The Youmapo complex consists of granodiorite (predominant phase) and muscovite-granite (supplementary phase). Traditionally, the supplementary phase was considered to be residual melt through fractionation of the predominant phase. However, our dating result by zircon LA-ICP-MS method show that the supplementary phase formed at 100.7 ± 0.5 Ma, which is significantly younger than the predominant granodiorite (109.0 ± 0.3 Ma). Other evidence further preclude the genetic relationship of fractional crystallization between the two units: (1) Hornblende, sphene and magnetite are common minerals in the granodiorite, suggesting water-rich and high oxygen fugacity features, which is different from the F-rich and low oxygen fugacity nature for the muscovite-granite as indicated by the presence of fluorite, ilmenite and sulfide. (2) Zircons from the muscovite-granite are characterized by extremely high U contents (10602 ppm), rugged surfaces and contain microfractures caused probably by radioactive damage, while zircons from the granodiorite have low U contents (860 ppm). (3) The muscovite-granite is enriched in Sr, Ba, Eu and LREE, and depleted in Na, Rb, Ga, W and Sn, with tetrad REE patterns and non-CHARAC behavior. Trace element modeling using Rb-Ba and Sr-Ba co-variations suggests that the supplementary phase is unlikely to be the derivative from the predominant phase via fractionation. (4) The predominant and supplementary phases have different Nd isotopic compositions (εNd(t) = -5.1~-4.0 and -9.6~-8.6, respectively). We conclude that the muscovite-granite probably formed through a new partial melting event related to basaltic underplating. High F contents reduced the solidus temperature and caused the highly evolved characteristics of the muscovite-granite. Therefore, the supplementary magmas have gone through intense interaction between melts and fluids, and played a significant role in W-Mo mineralization.