The deep ancient hydrocarbon accumulation in the Tarim Basin was extremely complex. It was characterized by large deep burial, multistage accumulations, multistage adjustments, and multistage secondary alterations, affording limited effectiveness of steroid/terpene biomarkers used widely in oil-source correlation. Aryl isoprenoids (AIs), as a series of diagnostic biomarkers, have attracted increasing attention. For a detailed investigation of AIs from the Lower Paleozoic strata and its internal crude oil in the Tarim Basin, various experimental techniques have been employed. The m/z 133 and 134 mass chromatograms of the AIs confirmed their identification. The anomalously heavy compound-specific δ13C (up to ∼ −16‰) indicated the unequivocal precursor of green sulfur bacteria that was only developed under photic zone euxinia (PZE) conditions. AIs were detected in highly mature source rocks and the crude oils suffered secondary alterations, indicating that AIs might have strong stability and anti-secondary-alteration ability. Based on their widespread distribution in the Lower–Middle Ordovician Heituao Formation (O1-2h Fm) and the Lower Cambrian Yuertus Formation (Є1y Fm) shales, the discovery of AIs in almost all crude oils suggests that the O1-2h Fm and Є1y Fm shales were the primary source rocks for the remarkably abundant Lower Paleozoic deep petroleum resources. This reverses the previously held belief that the Middle-Upper Ordovician source rocks were the primary source rocks. In addition, AIs might induce the formation of organic-rich source rocks (the TOC was up to 29.8%) by promoting high-quality preservation conditions (containing H2S). Furthermore, unlike the H2S poisoning mechanism for the end-Permian mass extinction explained by AIs, regionally distributed AIs triggered by H2S from non-volcanic eruptions could explain the biological radiations (such as the early Cambrian radiation). Therefore AIs might provide important insights into the research on deep ancient petroleum exploration and its contemporaneous biological events.