Neoproterozoic–Cambrian black shales are one of the most important hydrocarbon source rocks worldwide, including in the Shunbei and Fuman regions in the Tarim Basin, China. However, the hydrocarbon generation from these shales is complex, with liquid petroleum found in reservoirs at depths of 6000–8000 m. Based on drilling, seismic, and well testing data, the ultra-deep tectonic evolution of the northern Tarim Basin, and its effects on hydrocarbon generation from black shales were investigated. During the Neoproterozoic, the northern Tarim Basin was filled with rift and passive continental margin sedimentary rocks between the north and central Tarim paleo-uplifts. A sequence of lower Cambrian black shales was developed on the slope around the paleo-uplifts over a wide area, which are thick and have high contents of total organic carbon. Even after multiple stages of tectonism, including the Caledonian, Hercynian, Indosinian, Yanshanian, and Himalayan orogenies, the north (Tabei) and central paleo-uplifts were preserved. The Caledonian, Hercynian, and Himalayan orogenies were the main periods of hydrocarbon generation. Four hydrocarbon-generation models were established, which are the Tabei-, Bachu-, Tazhong-, and Tadong-types. The current Ro values of the Tabei-type black shales are 1.0%–1.5%, whereas those of the Bachu-, Tazhong-, and Tadong-type black shales are >2.0%. Due to the long-lived paleo-uplifts and short-lived deep burial during the Himalayan Orogeny, the Tabei-type black shale is in the oil and early gas generation stage, which obviously differs from the over-mature Cambrian and Ordovician black shales in South China. Therefore, the long-lived paleo-uplifts not only affected the deposition and distribution of black shale, but also hydrocarbon generation processes and the depth limit of active source rock. The thermal evolution of black shale in the ultra-deep Tarim Basin requires further investigation.