In order to clarify the fabrics of Cenozoic microbial carbonate and the genetic mechanisms of main rock forming minerals in the Qaidam basin, the petrographic classification, fabric identification, difference analysis of mineral morphological characteristics and Org- mineralization and biomineralization of microbial carbonates were studied by using a large number of core observation, thin section analysis, scanning electron microscope and electron probe analysis, and other analysis methods, focusing on the microbial carbonates of Youshashan Formation in Nanyishan- Dafengshan area. The analysis shows that the Youshashan Formation in Nanyishan area is developed with the thick layer of argillaceous carbonate rocks, with the thickness of 3~5 m; and the thin layer of microbial carbonates, with the thickness of 30~50 cm, the maximum thickness of microbial carbonates is about 2 m. It is considered that the microbial carbonates of Youshashan Formation in this area are mainly thrombolites and locally developed stromatolites. They are mixed and symbiotic. A large number of microbial fossils are found in the microbial carbonates by scanning electron microscope, which provides biological evidence for the formation of lacustrine microbial carbonates. The results showed that: ① The main mineral type of microbial carbonates is calcite, with complex micro morphology and various types, including spherical, agglomerates, rhombohedron and flaky structures. The distribution range of spherical particle size is 50 ~ 80 nm. The agglomerates are formed by polymerization and adhesion of several nano- sized spherical particles, and the particle size is several microns to tens of microns. Flaky calcite often varies in size and shape, with particle sizes typically ranging from 1 to 10 μm. ② A large number of calcified EPS fabrics and suspected microfossils were found, including spherical, short rod and filamentous fossils. The sizes of rod- shaped microbial fossils is about 0. 4 μm in diameter and 0. 5~1 μm long. Filamentous microbial fossil is about 0. 3~0. 5 μm in diameter and 1~2 μm long. ③ The formation of calcite minerals is mainly influenced by organic mineralization (or microbial induced mineralization) and biological mineralization. Among them, spherical calcite is mainly microbial induced formation, and a small amount of spherical calcite may be microbial controlled formation. The short rod- shaped and filamentous fossils maintain the morphological characteristics of microorganisms, which are mainly formed by microbial- controlled mineralization. ④ The formation of spherulites, agglomerates and agglomerates in the thrombolites may be formed by the calcification of the microbial film and its enclosed microbial colonies. The analysis shows that such minerals may be related to organic mineralization.