Carbonate rocks are the most widespread deposits in the marine facies, and also distributed in the lacstrine and arid exposed environments. Carbonate rocks of Lower Paleogene Kumugeliemu Group in Kuqa Depression deposited in the typical tide flat of semi-closed bay, a part of northern edge of Neo-Tethys Ocean. These carbonate rocks include gypsiferous dolomites deposited in upper-tidal flat, bioclastic shoal, bioarenitic bank, oolites deposited in the mid-tidal flat, micritic limestones, lime mudstones and micritic dolomites deposited in the lower-tidal flat. Blackish lenticular marlites of the lower part of Cretaceous Bashijiqike Formation deposited in the deep lacstrine, localized merely distributed in Well Kela 201. The grayish lenticular marlites of the middle part of Cretaceous Bashijiqike Formation were deposited in the arid exposed environment, merely distributed in Kuchehe Section. Lacustrine carbonate facies mostly distributed in Qiakemake Formation and secondly in Yangxia Formation and Kezilenver Formation. There developped stromatolitic limestones deposited in the high-energic littoral lacstrine environment in the upper of Jurrasic Qiakemake Formation in Kapushalianghe Section. Blackish micritic limestones frequently accreted with grayish mudstones. They were the results of deep to semi-deep lacstrine environments. These carbonate rocks deposited in the different periods and different environments possess the various disciplinary characters of trace elements and carbon—oxygen isotopes. It is important to interpret depositional environment variety and basin evolution for these carbonate rocks. The chemistry data’s deviation of individual sample cannot influence whole sedimentary environments distinguished. The depositional environments of Carbonate rocks should be distinguished by integrating sedimentary structures of associated rocks, sedimentary assemblages, paleotology, sedimentary geochemistry and etc.