The Tarim Basin is the only petroliferous basin enriched with marine oil and gas in China. It is presently also the deepest basin for petroleum exploration and development in the world. There are two main sets of marine Source Rocks (SRs) in the Tarim Basin, namely the high over-mature Cambrian–Lower Ordovician (∈–O1) and the moderately mature Middle–Upper Ordovician (O2–3). The characteristic biomarkers of SRs and oils indicate that the main origin of the marine petroleum is a mixed source of ∈–O1 and O2–3 SRs. With increasing burial, the hydrocarbon contribution of the ∈–O1 SRs gradually increases. Accompanied by the superposition of multi-stage hydrocarbon-generation of the SRs and various secondary alteration processes, the emergence and abnormal enrichment of terpenoids, thiophene and trimethylaryl isoprenoid in deep reservoirs indicate a complex genesis of various deep oils and gases. Through the analysis of the biofacies and sedimentary environments of the ∈–O1 and O2–3 SRs, it is shown that the lower Paleozoic high-quality SRs in the Tarim Basin were mainly deposited in a passive continental margin and the gentle slope of the platform, deep-water shelf and slope facies, which has exhibited a good response to the local tectonic-sedimentary environment. The slope of the paleo-uplift is the mutual area for the development of carbonate reservoirs and the deposition of marine SRs, which would be favorable for the accumulation of petroleum. Due to the characteristics of low ground temperature, the latest rapid and deep burial does not cause massive oil-cracking in the paleo-uplift and slope area. Therefore, it is speculated that the marine reservoirs in the slope of the Tabei Uplift are likely to be a favorable area for deep petroleum exploration, while the oil-cracking gas would be a potential reserve around the west margin of the Manjiaer Depression. Hydrocarbons were generated from various unit SRs, mainly migrating along the lateral unconformities or reservoirs and the vertical faults. They eventually brought up three major types of exploration fields: middle and lower Cambrian salt-related assemblages, dolomite inner reservoirs and Middle and Lower Ordovician oil-bearing karst, which would become the most favorable target of marine ultra-deep exploration in the Tarim Basin.