The petrogenesis of intermediate-silicic rocks with high Sr/Y ratios that are closely associated with porphyry Cu-Au mineralization and TTGs remains uncertain. This study presents new geochronological and geochemical data for high Sr/Y granodiorites and associated mafic microgranular enclaves (MMEs) from the Late Devonian–early Carboniferous Suanjingzi batholith in the Beishan orogen, NW China. The MMEs, dioritic and fine-grained, share mineral assemblages with their hosts but contain more amphibole. Similarities in ages and Sr-Nd-O isotopes between the MMEs and their hosts indicate that they share a common magma source. Our geochemical studies and quantitative modeling imply that upper crustal fractional crystallization of water-rich magma, represented by the associated MMEs, played a crucial role in forming the Late Devonian–early Carboniferous high Sr/Y rocks in central Beishan. High H2O contents promote amphibole crystallization and delay plagioclase appearance, giving rise to higher Sr and lower Y contents in evolved magma. Additionally, titanite fractionation can contribute to high Sr/Y ratios by decreasing Y contents. The MMEs, the best available proxy for the parental magma, originated from the partial melting of a mantle wedge metasomatized by subduction fluids. This study emphasizes the significance of upper crustal fractional crystallization of water-rich magma in forming high Sr/Y rocks. The possible increment caused by amphibole-dominated fractionation within the upper crustal level should be considered when employing Sr/Y ratios to quantify crustal thickness. Moreover, we argue that Late Devonian–early Carboniferous magmatism in central Beishan occurred in a continental arc setting, providing a stronger basis for understanding the Paleozoic tectonic evolution of the Beishan orogen.