Abstract: Objective The Lower Paleozoic Qiongzhusi Formation and Longmaxi Formation are the key strata for shale gas exploration and development in southern China. The organic matter content in the shale is a key index for determining the degree of gas enrichment. However, there has been a lack of systematic comparative study on the environmental control factors of organic matter enrichment in the two shales. Methods Using core/outcrop, X-ray diffraction, thin section, organic matter content, and element analysis data, the sedimentological and geochemical changes of the two shale layers were compared and analyzed. The differences in the sedimentary paleoenvironment between the two layers for similar geological backgrounds were systematically discussed, and the sedimentary paleoenvironment changes from passive continental margin to cratonic depression were compared and analyzed. The main controlling factors and differences of organic matter enrichment in two sets shale formations were clarified, and the corresponding enrichment models were established. Results （1） Vertically, the bottoms of the Qiongzhusi Formation（Q1 member） and Longmaxi Formation （LM1-LM5） are dominated by organic rich bio siliceous rock siliceous shale deposits, and the total organic carbon （TOC） content of the former is higher than that of the latter. At the top, with the continuous decline of sea level, TOC and biogenic silicon content showed a downward trend, whereas clay or carbonate rock mineral content exhibited an upward trend. Horizontally, under the control of paleogeomorphology, TOC and biogenic silicon content decreased from passive continental margin to cratonic depression in different sedimentary periods. （2） The high TOC shale sections at the bottom of both shales were formed in environments with low terrestrial input, high paleoproductivity, and good preservation conditions. Moreover, the paleoproductivity level and bottom water reduction degree of the Q1 member were higher than those of LM1-LM5, resulting in higher TOC content. With the continuous decline of sea level, both shales exhibited increasing terrigenous input and worsening preservation conditions, but the changes of paleoproductivity are significantly different： in the Qiongzhusi period, ocean current activity weakened with the decline of sea level, and the level of paleoproductivity decreased. In the Longmaxi period, the flexural-migration led to the gradual opening of the northern barrier in the Yangtze Basin, and the scale of ocean current influx gradually expanded. Weakly affected by sea level decline, the level of paleoproductivity increased. Vertically, the TOC content of the Qiongzhusi Formation was primarily controlled by the reduction of paleoproductivity, deterioration of preservation conditions, and increase of terrestrial input, whereas the Longmaxi Formation was controlled by the latter two factors. Horizontally, the two shales transitioned from the passive continental margin to the cratonic depression, and the sea level height and upwelling current activity decreased. The preservation conditions and paleoproductivity level became worse at the same time, and the TOC content decreased accordingly. （3） Controlled by the sedimentary paleogeographic background, the exploration and development of shale gas in the Qiongzhusi Formation should focus on the southwest, whereas Longmaxi Formation should focus on the northwest. The organic matter enrichment environment gradually improved in the southwest direction during the Qiongzhusi stage, and the thickness of the organic matter rich shale increased near the tensile rift center, whereas the organic matter enrichment environment became better in the northwest direction during the the Longmaxi stage, and the sedimentary center gradually migrated to the northwest due to foreland flexus-migration, and the thickness of the organic matter rich shale increased. Conclusions This study can provide a reference for further exploration of the accumulation mechanism for organic matter in Lower Paleozoic Marine shales, guiding shale gas exploration.