The Ningshan pegmatite district in the South Qinling Orogen hosts numerous Rb-(Be) mineralized pegmatites. In this study, whole-rock geochemistry, mineral geochemistry, and zircon U–Pb isotopes of the Rb-rich and barren pegmatites were determined. The barren pegmatites consist mainly of muscovite, microcline, albite, quartz, and garnet, whereas the Rb-rich pegmatites are mainly composed of muscovite, albite, quartz, and beryl, with minor chrysoberyl, cassiterite and columbite-group mineral. The muscovite and albite are the main Rb-bearing minerals. The U–Pb zircon dating of the Rb-rich and barren pegmatites yielding an age of 212–203 Ma, which is similar to that of the neighboring two-mica monzogranites distributed in the Ningshan area. Compared with the two-mica monzogranites, geochemical features, such as the Zr/Hf, Rb/Sr and Nb/Ta ratios and trace element contents indicated that the Rb-rich and barren pegmatites derived from fractionation of the two-mica monzogranites. In combination, the current and previous results suggest that the fractionation of the two-mica monzogranites caused the generation of the affinitive residual melts that, finally, crystallized to form the pegmatites. Compared to those from the barren pegmatites, the apatite from the Rb-rich pegmatites have higher MnO (14.51–19.12 wt.%) and Cl (0.12–0.16 wt.%) contents and lower F/Cl rartios (20–29). We conclude that these differences reflect unique geochemical signatures, and the geochemical composition of the apatite can be used as exploration guidance for rare metal-rich pegmatites.