The Koktokay No.3 pegmatite dike was formed in the Late Triassic (similar to 220Ma), and the muscovite-albite granite intruded into the Koktokay No.3 pegmatite was formed in the Early Jurassic, while the Aral granite which was contemporaneous to the Koktokay No.3 pegmatite dike was not a rare-metal parent granite. Therefore, the Koktokay No.3 pegmatite dike can not be the product of granite differentiation, but from anatexis of metasedimentary rocks. The Koktokay No.3 pegmatite dike is characterized by low zircons epsilon(Hf)(t) (+1.25 similar to+2.39) and delta O-18 (7.57 parts per thousand similar to 8.85 parts per thousand) values, indicating that its source is a mixture of juvenile crust and ancient crust. The Koktokay No.3 dike has undergone magmatic stage (I-IV zones), magmatic-hydrothermal transition stage (V-VIII zones) and hydrothermal stage (IX zone), in which the magmatic-hydrothermal transition stage was characterized by coexistence of crystal, melt and fluid after 70% fractional crystallization of pegmatite-forming magma. The highly differentiated pegmatites are characterized by obvious internal textural zonation, in which the textural units were components of the pegmatites and associated to the disequilibrated crystallization under liquidus undercooling and hydrothermal alteration. The Be mineralization occurs mainly in the zones of I, II and IV, while the Li mineralization occurs mainly in the zones of V, VI and VIII, indicating that beryllium and lithium ore bodies in the Koktokay No.3 pegmatite dike were formed during the magmatic stage and the magmatic-hydrothermal transition stage, respectively. As there is mineral paragenesis of plate-like beryl with skeletal crystal apatite, garnet and a small amount of muscovite, metallogenic mechanism of Be for beryl saturated crystallization in the II zone of the Koktokay No.3 pegmatite dike was attributed to ASI changes in melts before and after apatite crystallization. From early to late textural zones, the K/Rb ratios in alkaline feldspars and muscovites decrease as the Li, Rb and Cs contents increase, and the Zr/Hf ratio in zircon decreases as Hf contents increase, indicating fractional crystallization is the main mechanism for Li supernormal enrichment in pegmatite-type lithium deposits.