Although the metallogenic mechanism of the Jiajika super-large Li deposits in the eastern Tibetan Plateau has been proposed closely linked to development of the Majingzi granite pluton, the petrogenesis and evolutionary linkages between granite–pegmatites and Li mineralization still remain controversial. Here we investigated Li-Nd isotopes together with major and trace elemental data from a 3-km scientific drillcore and surface samples (including the Li-rich/poor pegmatites, the associated two-mica granite and the metasedimentary rocks) to reveal the magmatic evolution and Li-enrichment mechanism of the Jiajika deposit. In the drillcore, the Li-poor pegmatites overall exhibit low Li isotope values (δ7Li = −1.38 ‰ to +1.98 ‰, mean of +0.34 ‰) and low Li contents (67 to 45 ppm), while the Li-rich pegmatites show slightly higher δ7Li values (+0.9 ‰ to +1.1 ‰) and high Li contents (3078 to 6012 ppm). Additionally, the Li-poor pegmatites have εNd(t) values of −17.1 – −2.5 (mean of −10.34) and low Nd concentration (<10 ppm), similar to the two-mica granite (εNd(t)avg = −11.18 and Ndavg = 7.08 ppm), whereas the schists and calc-silicate rocks in the drillcore have relatively higher εNd(t) values (−11.9 to −2.4 with a mean of −7.3) and Nd contents (>20 ppm). These data, together with consistently low Nb/Ta、Zr/Hf of the deep-drilled pegmatites and two-mica granites, suggest that the Jiajika pegmatites are not directly derived from low degrees of partial melting of the Triassic metasediments (e.g., biotite shists or calc-silicate rocks), but more likely from extreme magmatic fractional crystallization of the Majingzi two-mica granite pluton. For the surface samples, the δ7Li values of the surface Li-poor pegmatite samples (−0.61 ‰ to +2.56 ‰ with a mean of +0.36 ‰) are slightly higher than that of the Li-rich pegmatites (−0.52 ‰ to −0.27 ‰ with a mean of −0.39 ‰), and the two-mica granites samples show relatively variation in δ7Li (−1.25 ‰ to +3.33 ‰ with a mean of +0.73 ‰). The surface granites and pegmatites are characterized by high A/CNK values (>1.1) and low K/Rb values (<200), and particularly, the degree of REE tetrad effect gradually increases from granites to pegmatites. We suggest that the Majingzi two-mica granites exposed by the Jiajika gneiss dome is analogous to the deeper granitic sheet implied by the 3 km deep drilling, which both are strongly peraluminous S-type granites with a highly fractionation. Based on the degree of evolution of the Li-rich, Li-poor pegmatites and the two-mica granites and other geochemical evidence, we used a Rayleigh fractionation model to reproduce Li isotope variations in different types of rocks around the Jiajika deposit, suggesting an extreme magmatic differentiation without significant fluid exsolution as the origin for Li enrichments in pegmatites.