Abstract: The rift stage (Barremian-Aptian of the Early Cretaceous) of the Santos Basin in Brazil is characterized by the development of world-class large-scale lacustrine carbonates deposition. At present, numerous oil and gas discoveries have been made in this field, making it a hot spot for global oil and gas exploration. The development degree of carbonate sediments is the key to the enrichment and accumulation of oil and gas in the basin. Drilling results reveal the development of "two phases and two types" of lacustrine carbonate sediments during the rift stage of the basin: shell limestone of Itapema (ITP) group in early fault-sag depression transition period (Late Barremian-Aptian) and microbial reef limestone of Barra Velha (BV) group in late sag depression period (Mid- Late Aptian). Although both of these "two phases and two types" lacustrine carbonate sediments are biogenic limestone, their genesis mechanisms and lithological combinations differ significantly. In order to clarify the sedimentary differences and main controlling factors of the " two phases and two types " lacustrine carbonate rocks, based on thin section, core, logging, seismic and other data, this paper conducts a systematic petrological and sedimentological study of two types of lacustrine carbonate sediments in the basin, combining micro and macro perspectives. Comprehensive research shows the development of large-scale lacustrine carbonate sediments in the Lower Cretaceous of the Santos Basin in Brazil is mainly controlled by paleogeomorphology, paleolake water salinity and paleowater energy changes. Paleogeomorphology controls the distribution and development of sedimentary microfacies of lacustrine carbonate reservoirs, paleowater salinity controls the vertical evolution of lacustrine carbonate sediments types, and paleowater energy and water depth control the microfacies variation of lacustrine carbonate sediments. Finally, it was confirmed that the high-energy freshwater environment in the face of waves is a favorable background for the development of shell limestone reservoir in Itapema Formation, and the shallow medium-high energy semi saline - saline water environment in the face of waves is a favorable background for the development of stromatolitic limestone reservoir in Barra Velha Formation. This points out the directions for finding favorable reservoir development zones and has practical guiding significance for the oil and gas exploration in lacustrine carbonate rocks of Brazil.