A maturity sequence from the Keluke Formation of the Upper Carboniferous marine-continental transitional depositional environment in the Qaidam basin, NW China has been geochemically characterized by bulk and molecular compositions, especially the behavior of polyaromatic hydrocarbons and organosulfur compounds. Some commonly used maturity parameters such as the methylnaphthalene ratio (MNR), the dimethylnaphthalene ratio (DNR), the methylphenanthrene ratio (MPR), methylphenanthrene index-3 (MPI-3), dimethylphenanthrene index-2 (DMPI-2), the methyldibenzothiophene ratio (MDR) and dimethyldibenzothiophene (DMDBT) ratios (4,6-/1,6- + 1,8- + L,4-DMDBT and 2,4-/1,6- + 1,8- + L,4-DMDBT), Rock-Eval T-max, and measured vitrinite reflectance (%R-o) increase gradually with burial depth, whereas others such as the trimethylnaphthalene ratio (TMNr), the tetramethylnaphthalene ratio (TeMNr), MPI-1, and DMPI-1 show no correlation with these maturity indicators. The calculated equivalent R-o values from MPR and MDR based on empirical correlation reported in the literature overestimate the maturity level. The degree of alkylation plays a dominant role in molecular compositional variation and maturity parameter validity, which is in turn controlled by the nature of organic input, depositional environment, and lithology rather than solely controlled by maturation. Dealkylation of alkylnaphthalenes at R-o similar to 1.0% removes most thermally unstable isomers from C3- and C4 homologues, which makes parameters based on them lose sensitivity. The proportion of phenanthrene varies greatly in the marine-continental transitional depositional system and the involvement of phenanthrene in the formulation makes MPI-1 and DMPI-1 fail to reflect the maturity level. Overestimation of the maturity level based on the degree of isomerization is caused by a high catalytic effect in the marine continental transitional depositional system, which facilitates isomerization and dealkylation processes.