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Fifty samples from the source rocks in Member 3 and Member 4 of the Paleogene Shahejie Formation in the Bohai Bay Basin, East China, were analyzed to investigate the distribution, evolution of the molecular maturity ratios C₂₉ββ/(ββ+αα) and C₂₉20S/(20S+20R) and their control factors in the natural geological profile and sequence. The results showed that progressive changes in molecular maturity parameters are associated with major changes in thermal evolution of related biomarkers. Increases in the C₂₉ββ/(ββ+αα) and C₂₉20S/(20S+20R) ratios result from the difference in the relative rate between generation and thermal degradation of isomers involved. The samples from a hyper-saline environment below 3.5 km in which evaporitic rocks deposited shows high response of Sr/Ba, Sr/Ca, Fe/Mn, Pr/n-C₁₇, Ph/n-C₁₈ and gammacerane and low response of Pr/Ph. There presents negative reversal of biomarker maturity C₂₉ββ/(ββ+αα), C₂₉20S/(20S+20R) and Ts/(Ts+Tm) in the samples from hypersaline environment, reflecting that the gypsum- halite have negative effect on the isomerization of biomarker and thermal evolution of organic matter. The minerals in evaporites also retard the conventional thermal indicators including vitrinite refl ectance (R_o) and pyrolysis peak temperature T_max at the depth below 3.4 km (i.e. >3.4 km), and these parameters also show the inhibition from overpressure in the range of 2.4-3.4 km. This result will be helpful in the interpretation and application of molecular maturity parameters for similar saline lacustrine basins