Abstract <p>Source rock from the Huoshiling Formation in the southern Songliao Basin is of particular significance, as it is a critical contributor of deep layer natural gas, which has become one of the exploration targets in this region. However, knowledge of its geochemical characteristics is largely limited, which is further insufficient to address the substantial heterogeneity of different sub-sags which are separated by faults during the rifting stage. In this study, we conduct organic geochemical analysis using gas chromatography-mass spectrometry (GC-MS) of Huoshiling Formation source rock retrieved from sub-sags namely Baojia, Guojia, Huajia, Lanjia and Nong’an South in Dehui fault depression and Xiaochengzi sub-sag in Wangfu fault depression, southern Songliao Basin. The results obtained demonstrate that the biomarker of source rock displays substantial variation, particularly in the distribution of <i>n</i>-alkanes, steranes and hopanes, indicating organic matter originating from different sources in the sub-sags. Combining bulk geochemical data, we propose that source rock in Dehui and Wangfu fault depression could be classified into three categories, each exhibiting a comparatively elevated proportion of organic matter derived from algae, terrestrial plants and bacteria, respectively. This is found to be intimately linked to the source rock quality. Particularly, Nong’an South sub-sag is characterized by elevated levels of both the sterane/hopane ratio and the C₂₇ sterane percentage, indicative of remarkable algae input which results in better quality of higher hydrocarbon generation potential and saturated hydrocarbons when compared to other studied sub-sags. This provides valuable insight into the exploration of the deep layer in the southern Songliao Basin.</p>