The early Precambrian khondalite series is widely distributed in the Jining-Zhuozi-Fengzhen- Liangcheng area, southeastern Inner Mongolia. The khondalite series mainly consists of sillimanite garnet potash feldspar (or two-feldspar) gneiss and garnet biotite plagioclase gneiss. These gneissic rocks have commonly experienced granulite-facies metamorphism. In zircons separated from sillimanite garnet potash feldspar gneisses, many mineral inclusions, including Sil, Grt, Ky, Kfs, Qtz and Ap, have been identified by the Laser Raman spectroscopy. Generally, prograde metamorphic mineral inclusion assemblages such as Ky + Kfs + Qtz + Ap and Ky + Grt + Kfs + Qtz are preserved in the core of zircon, while peak granulite-facies metamorphic minerals including Sil + Grt + Kfs + Qtz and Sil + Grt + Kfs + Qtz + Ap are identified in the mantle and rim of the same zircon. However, in some zircons are only preserved the peak metamorphic minerals such as Sil + Grt + Kfs + Qtz and Sil + Grt + Kfs + Qtz + Ap from core to rim, and in others are inherited the primary cores with minor mineral inclusions of Kfs + Qtz, with peak metamorphic mineral inclusions around the inherited cores. These data indicate that the mineral assemblage evolution of sillimanite garnet potash feldspar gneisses in the study are did experience a polymorphic transformation of kyanite to sillimanite. In garnet biotite plagioclase gneisses, secondary electron microscopic images reveal that most zircons display distinct zoning textures, which comprise cores and rims, each with distinctive inclusion assemblages. The inherited mineral inclusions, mainly consisting of Kfs + Pl + Qtz, Kfs + Qtz and Kfs + Qtz + Ap, are preserved in the primary cores, while peak granulite-facies mineral asemblages, including Grt + Bt + Pl + Qtz + Ap, Grt + Bt + Pl + Qtz and Grt + Bt + Pl + Qtz + Rt, are identified on the rims. The occurrence of peak metamorphic mineral inclusions in zircons indicates that these gneissic rocks, including sillimanite garnet potash feldspar gneiss and garnet biotite plagioclase gneiss, have experienced granulite-facies metamorphism.Secondary electron microscopic images of zircons from the khondalite series display distinct zoning from core to rim, and are genetically related to the primary, prograde, and peak metamorphic mineral inclusion assemblages respectively. These images reveal irregular zoning patterns and varying thickness of cores and rims. The abundance of inclusions complicates the conventional U-Pb age dating. Therefore, the SHRIMP micro-spot U-Pb method is essential for the protolith and metamorphic age dating of the khondalite series, southeastern Inner Mongolia.