In this study, we conducted systematic analysis of total organic carbon (TOC) content, lipid biomarkers, carbon isotopes of kerogen (δ13Ckerogen), and mineral composition in Niu-ti-tang (Є1n) and Pa-lang (Є1p) shales from Guizhou Province in order to provide a better understanding of the organic sources and marine environmental condition during deposition of the Lower Cambrian shales of South China. The results show that a broad variety of lipid biomarkers, such as n-alkanes, pristane, phytane, terpanes, hopanes, and steranes, are in these shales, which suggests a significant contribution of various paleobios with bacterial microorganisms and algae thriving under a low-salinity and stable anoxic environment. The negative δ13Ckerogen value (minimum −36.4‰) and occurrence of pyrite (1–7.5%) and carbonates (2.4–57.3%) indicate that bacterial sulfate reduction prevailed under anoxic conditions during deposition of the Lower Cambrian shales. Moreover, the difference in mineral and δ13Ckerogen composition between Є1n and Є1p shales might imply significant changes in primary production and paleoocean environments due to sea-level rise, as shown by the higher average TOC content in Є1p shales (2.52%) compared to that in Є1n shales (1.79%). The covariances of TOC content and mineral and δ13Ckerogen composition suggest that the Є1p shales might have been deposited under a higher sea level associated with high primary productivity, compared to Є1n shales. Thus, high primary productivity driven by sea-level rise is suggested to be the main controlling factor on organic matter enrichment in Є1p shales under stable anoxic conditions.