The degree of thermal alteration of organic matter in sediments is crucial for comprehending the progress of oil and gas generation. The thermal maturity of kerogen, which is a component of the organic matter in source rocks, has been extensively studied in early Cambrian strata in the Yangtze Platform. For example, the gas generation potential of the kerogen was determined to be at a mature to over-mature stage. However, there has been relatively less focus on the extractable organic matter. The recognition of extractable organic matter as a source of secondary gas generation has been made in the context of over-mature sediments. The thermal maturity of extractable organic matter is crucial for its interpretation, as is the mineralogy resulting from burial modification, because of the interaction of mineralogy with maturity. Gas chromatography-mass spectrometry analysis was conducted on aromatic compounds from early Cambrian sediments in Yunnan Province. The aromatic compounds were found to possess a preference for β-substituted isomers that are more thermally stable. The ratios determined from alkylated naphthalenes and phenanthrenes, which are reliant on thermal maturity, provided a consistent distribution throughout the different burial depths. However, alkylated biphenyls and alkylated dibenzothiophenes have variable trends, with anomalously lower thermal maturity in the deeper buried sediments. The interaction of aromatic compounds and clays as a function of thermal modification was tested through the use of scanning electron microscopy, with correlation analysis of temperature-dependent aromatic ratios and clays. The correlation coefficients between an illite-associated ratio and thermally-dependent alkylated biphenyl and dibenzothiophene ratios are above 0.9. Our hypothesis is that the process of illitisation hindered the thermal alteration of alkylated biphenyls and dibenzothiophenes.