In view of the problems that the lack of a systematic microbialites classification, the uncertain of facies significance of different microbialites types and the lack of sedimentary models, this paper made a series of detailed study on petrology and rock assemblage sequence of two Proterozoic profiles and three Phanerozoic profiles in Tarim, Sichuan and Ordos Basins, acquiring three achievements and understanding: (1) Establish a new microbialites classification based on structure scale and morphological characteristics which is more systematic. (2) Make out the facies significance of the microbialites: laminated carbonate is the dominant type below the storm wave base; foamed and crumbed thrombolites, and domed, tapered, columnar stromatolites are mostly developed between storm wave base and normal wave base; wavy stromatolites are mostly developed between normal wave base and average low tidal base; and the lime-mud mound, sheet-like and mound-like microbial carbonates mainly exist in tidal flat environment over the average low tidal base. (3) Establish two microbialite sedimentary models for ramp sedimentary system and rimmed sedimentary system. These understandings are of great significance for reconstruction of lithofacies palaeogeography and prediction of reservoirs distribution of microbial carbonate.