The Barerzhe alkaline granite bearing a supergiant REE-Nb-Be-Zr deposit locates in the middle of the Xing' an-Mongolia orogenic belt of Northeast China. Using cathodoluminescence, electron microprobe and LA-ICP-MS analysis, nineteen grains of light-colored zircon and the dark-colored zircon from the East body ( ore body) of the Baerzhe alkaline granite have been tested in this paper, and the relationship between petrological genesis and mineralization were discussed. The two type's zircons of the light-colored zircon and the dark-colored zircon crystals present different CL characteristics. For the former, wide discontinuous oscillatory zoning can be present, and the core-mantle zoning zircon also can be found in some grains; The latter has more developed dissolution structures at its rim or internal pits and cracks than the former, indicating that the involvement of fluids in the formation of the dark-colored zircon is more obvious. Both two types of zircon are rich in Nb, U, Y and REE, but the dark-colored zircon has higher Fe content. The type I of Light-colored zircon has the features of LREE enrichment, clear HREE differentiation, high Hf, Nb, Ta content and the low Y content; The type II of Light-colored zircon is poor in LREE with unobvious HREE differentiation, and its REE chondrite distribution pattern have obvious "M-type" tetrad effect, indicating that zircon crystallized in melt-fluid system. The primary region of dark-colored zircon shows similar REE patterns to the type I[ of Light-colored zircon with LREE poor and unobvious HREE differentiation. The Sigma REE of altered part has no significant changes, but its LREE and Nb, Ta, U, Th content and Th/U ratio decreased. Both types have nearly Pb-206/U-238 nearly the same b/U age and the calculated age is 122. 7 +/- 1. 8Ma ( MSWD =5. 1), similar to the previous data by Rb-Sr and UPb isotope analyses. The above-mentioned results show that Baerzhe syn-minerogenic zircon has the characteristics of mantel source. The enrichment and metasomatism of the source and fractional crystallization of the melt with aqueous hydrothermal fluids rich in F and Cl resulted in the enrichment of metallogenic element of rare and rare-earth metal leading to the formation of supergiant deposit.