Understanding fractionation of silicic magma is crucial to advance our knowledge of differentiation of continental crust, enrichment of elements of economic interest, and plutonic–volcanic connection. Microstructural records afford critical appraisals for silicic magma fractionation, yet are rarely reported in granite plutons. Here we combine detailed microstructural observations and thermodynamic modeling to quantify the components and the conditions of silicic magma fractionation using the peraluminous Jiuzhou pluton (South China) as an example. The pluton shows compositional gradients from primitive orthopyroxene-bearing granite (charnockite) at stratigraphically low levels to relatively evolved orthopyroxene-free granite at stratigraphically high levels. Deviation of whole-rock compositions from metasediment-sourced experimental melts, and step-zoned plagioclase and alkali feldspar crystals in the exposed rocks suggest open-system fractionation by melt extraction, partial dissolution, and subsequent crystallization from trapped minimum melt. Crystal cluster and chain fabrics and viscous deformation are more abundant in the charnockites than in the overlying orthopyroxene-free granites, suggesting that gravitational, compaction-driven fractionation increased towards the bottom of the pluton. Field observations, thermodynamic modeling and petrographic studies further demonstrate that gravitational compaction reduces the trapped melt fraction of a crystal mush with thickness of ≥100 m from ∼30 wt% at the upper level to ∼10 wt% at the lower level of the pluton. Significant melt extraction restricted back-reaction with high-temperature phases during progressive crystallization, which preserved orthopyroxene during the solidification of granitic magma. The compositional, mineralogical and textural zoning of the Jiuzhou pluton suggests that incremental fractionation of granite systems may be an important process that produces compositionally zoned cumulate. Incremental fractionation may occur in many zoned granite plutons worldwide, causing their whole-rock composition to deviate from their primary melt composition. Detailed microstructural examination for these granite plutons may provide insights into the mechanism(s) for melt extraction and crystal accumulation of silicic magma, providing key insights towards quantifying fractionation of magma systems.