Abstract: The Permian source rocks in the South Yellow Sea Basin (SYSB) are characterized by multi-sets of hydrocarbon-generating strata, high thermal evolution degrees, and dramatic changes in sedimentary environment. However, at present, little is known about the biomarker differences of the source rocks. Through organic geochemical analysis with 16 mature to over-mature source rock samples in the four sets of Permian source rocks of the CSDP-2 well in the SYSB, the compositions, evolution law, and geological significance of biomarkers in the alkane and aromatic hydrocarbon fractions are clarified. Biomarker parameters show that the relative abundance of the compounds in sterane series, triarylsterane series, alkyl dibenzothiophene series, and the β-carotene varied greatly in different sets of source rocks in the Permian of SYBS. Three types of source rocks could be classified, namely, mudstones in the Lower Qixia Formation and the Longtan to Dalong Formation, chert in the Upper Qixia to Gufeng Formation, and siliceous mudstones in the Gufeng Formation. The research proved that mudstones in the Lower Qixia Formation, the Longtan Formation, and the Dalong Formation are deposited in oxic fresh or dysoxic brackish water conditions, in which the organic matter mainly derived from plankton and terrestrial higher planters. Source rocks in the Upper Qixia Formation and the Gufeng Formation are deposited in anoxic saline or euxinic sulfidic environment, in which the organic matter in chert is derived from plankton and diatom, whereas that in siliceous mudstones is derived from plankton, diatom, and terrestrial higher planters. Besides that, we proposed that the methylphenanthrene indexes and the alkyl dibenzothiophene parameters (4-MDBT/DBT, MDBI, 4,6 -/1,4-DMDBT) could be used as maturity scale for the Upper Permian source rock, but cannot be used for the Middle and Lower Permian source rocks.