The intricate relationship between climate and vegetation dynamics, particularly during the late Paleozoic ice age marked by multiple icehouse-greenhouse transitions, is a compelling aspect in Earth's historical narrative. In this study, we decipher the interactions between the Permo-Carboniferous climate fluctuations and floral turnovers within the North China Craton, based on the stratigraphic distributions of biomarkers and carbon isotopes from cored coals in Huainan coalfield, North China. Our findings reveal that the changes in n-alkane, terpane, sterane, and polycyclic aromatic hydrocarbon (PAH) distributions result from a confluence of maturation, depositional environment, and organofacies effects. Molecular maturity-sensitive ratios align with the maturity stage determined by Rock-Eval pyrolysis and petrography, categorizing the coals as high volatile bituminous A/B with a composite organic matter derived from terrestrial plants and marine algae. Notably, the 18α-22,29,30-trisnorneohopane (Ts) to 17α-trisnorhopane ratio (Ts/(Ts + Tm)), as well as C31–C34 22S/(22S + 22R) hopanes and C29 20S/(20S + 20R) steranes ratios exhibit moderate correlations with %Ro, indicative of epimerization reactions induced by maturation processes. The stratigraphic variations in pristane to phytane ratios (Pr/Ph), Pr/n-C17, Ph/n-C18, C30 αβ/(αβ+βα) hopanes, and organofacies sensitive PAH indices collectively capture a paleoenvironmental shift from reducing to oxic conditions attributed to marine regression. The systematic changes in PAH concentrations and their maturity indices reflect condensation and dealkylation reactions during the maturation process. The δ13C signature manifests a negative excursion in coals of the Artinskian Shanxi Formation and a subsequent positive excursion in the Capitanian Upper Shihezi Formation coals, respectively, reflecting changes in the δ13C values of contemporaneous atmospheric CO2 in response to regional aridity fluctuations.