Abstract: In recent years, microbial carbonate reservoir development technologies are the research frontier all over the world, with a certain number of achievements and cognition, while the refined reservoir description is relatively weak. Taking Cretaceous lacustrine microbial carbonate oil field in Santos Basin as an example, the authors in this paper have used outcrop, core, logging and seismic data to comprehensively analyze the lithologic characteristics, sedimentary, physical characteristics and main controlling factors in the study area. And the internal structure of the reservoir was classified and described, and the quantitative characterization method was thus established. The results show that: ① The study area was composed of three independent carbonate platform deposits, which could be subdivided into four subfaces: microbial limestone mound, high-energy grain bank, inter-mound depression and inter-platform depression. ② Microbial limestone, bioclastic granular limestone, scale granular limestone and stratified rock were the main reservoir rock types. ③ The reservoir was with good physical properties: the porosity was 4%-27% with an average of 12.5%, and the permeability was (0.01-3 000)×10^-3 μm² with an average of 120×10^-3 μm². ④ The development of reservoir was influenced by sedimentation and diagenesis, and the development of dominant reservoir was controlled by paleo structure. The effect of quasi-syngenetic dissolution on reservoir transformation was strengthened, and the bioclastic particles by periodic exposure and dissolution were filled into the inter-mound depression to form the high-porosity and high-permeability bands. ⑤ The inner structure of the reservoir in the study area was based on microbial limestone mound groups, which were subdivided into mound foundation, mound core, mound wing, inter-mound, and inter-mound sweet spot. The quantitative characterization method of cluster assemblage model had been established based on sedimentary facies and controlling factors of diagenetic facies, which has achieved good application effects in oil field development.