Granitic melt composition is controlled by melting reactions and modified by melt segregation process. This is a fundamental but unresolved issue for granite petrogenesis. To investigate the influence of these two processes on granitic melt compositions, we conducted systematic petrographic and geochemical analyses of melanosome and leucosome samples from the Jindong migmatite in the Indosinian orogen, South China. Petrographic observations and zircon U-Pb geochronology indicate that the Jindong migmatite was formed through water-fluxed melting of the Early Paleozoic gneissic granite (437±2 Ma) during the Triassic (238±1 Ma). The Jindong leucosomes can be divided into lenticular and net-structured types. They show increasing Rb with decreasing Ba and Sr, due to fractionation of K-feldspar and plagioclase during melt segregation. Nd isotope and Th, Y and REE contents of leucosomes reveal the complex behavior of phosphates during melting, recorded by the incongruent melting of apatite with precipitation of monazite and xenotime in the source. The leucosomes have similar Nd isotopic compositions with the source due to early dissolution of monazite. Continued dissolution of apatite caused saturation of monazite and decreased εNd(t) values of melts. This interplay also caused sharply reduction of Th, Y and REE contents in melts with increasing P2O5, when saturation of monazite and xenotime due to dissolution of apatite. Thus, dissolution of accessory phase in the source impacts fundamentally on REE geochemistry and Nd isotope of granites. Such patterns are reflected in granites worldwide, illustrating the strong controls of the melting and melt segregation processes on granitic melt compositions.