The age distribution of lithium-cesium-tantalum (LCT) pegmatites largely overlaps with major phases of collisional orogenic events and assembly of supercontinents. Some of the largest known LCT pegmatite deposits formed in very short intervals, 2.7–2.5 Ga and 1.9–1.8 Ga, corresponding to two major pulses of continental crust growth. However, the exact process of generation and segregation of large volumes of Li-bearing pegmatite liquids, perhaps involving disequilibrium fractional crystallization and leaving residual melts enriched in fluxing elements such as B, F, H2O, Li, and P, remains obscure. The new data on Li contents and isotope compositions in major mineral phases from temporally and geographically separated pegmatite bodies document extreme variations in δ7Li values among individual large LCT pegmatite bodies, in particular Archean occurrences. The observed >10‰ variations in δ7Li values for the same mineral phases from different localities (i.e., beryl, petalite, spodumene, lepidolite, amblygonite, muscovite) contrast with globally homogeneous Li isotope systematics of major mineral phases from unmodified mantle rocks. Consistent Li isotope offsets between coexisting mineral phases are best explained by Li isotope fractionation as a function of the bond length between Li and neighboring ions (O, OH, F). We suggest that spatially distinct Li isotope patterns act as fingerprints for different pegmatites and can be explained by the preexisting Li isotope differences of their crustal sources at the time of pegmatite formation owing to differences in crustal age and evolution. This would imply secular evolution of the continental crust over Earth history toward present-day globally broadly uniform crustal 7Li/6Li ratios (δ7Li ∼0‰). The differences among Archean occurrences could reflect possible Archean paleogeography and could be linked with different thermal regimes of individual cratons as a consequence of variations in crustal thickness. One possible application of the new data set may be in source verification of gem-quality stones by using Li isotopes.