Abstract: Deep to ultra-deep hydrocarbon reservoirs are characterized by prolonged fluid evolution processes and complex accumulation mechanisms. The Tarim Basin represents the most typical deep to ultra-deep exploration and development area in China. To date, only a few wells have revealed the hydrocarbon source rocks and reservoirs in the Sinian–Cambrian strata of the Lower Paleozoic. However, the lack of direct isotopic chronological studies on hydrocarbon migration and accumulation from source to reservoir in the Sinian–Cambrian strata limits our understanding of hydrocarbon accumulation mechanisms in the ultradeep layers of the Tarim Basin. This study focuses on vein fillings within pore-fracture systems in source–reservoir intervals, including the Cambrian Yurtus Formation and the Sinian Qigebulak Formation, to determine the origins and genesis of multiphase veins. Based on fluid inclusion analyses combined with U-Pb and Re-Os isotopic dating, the dynamic process of hydrocarbon accumulation in deep reservoirs is elucidated. The results show that the two stages of calcite veins in the source rocks of the Cambrian Yuertusi Formation in the northern Tarim Basin are hydrothermal and show the source of deep strontium-rich fluids. Two periods of dolomite pore-filling veins are developed in the corresponding Sinian Qigebulake Formation reservoir. The rare earth element distribution pattern shows that the two periods of fluids in the reservoir show the source of diagenetic fluids, and the strontium isotope of the second period of dolomite veins shows the source of Cambrian seawater at the same time. The first stage of calcite veins ( 466 ± 5 Ma ) in the source rock of the Yuertus Formation and the first stage of dolomite veins ( 460 ± 10 Ma ) in the reservoir of the Qigebulake Formation were both formed in the Middle Ordovician. With the deepening of burial, the source rocks entered the oil generation threshold in the Carboniferous, and the first stage of crude oil filling occurred in the Permian ( Hercynian ). The oil inclusions captured in the veins confirmed a good source-reservoir matching relationship. A large number of oil inclusions were captured by the second stage calcite veins ( 263 ± 69 Ma ) of source rocks and the second stage dolomite veins ( 55 ± 15 Ma ) of reservoirs. The analysis of burial history indicates that the large-scale filling occurred in the Miocene, which realized the high coupling of hydrocarbon generation and accumulation in time and space. A large amount of solid residual asphalt ( 30 ± 14 Ma ) was developed in the dolomite veins in the reservoir later than the second stage, indicating that the oil and gas destruction and adjustment process occurred in the early Oligocene of the Sinian oil and gas reservoirs, corresponding to the tectonic uplift in the Himalayan period. Through the systematic isotope chronology study and fluid evolution analysis of the deep source reservoirs in the Tarim Basin, the hydrocarbon generation, hydrocarbon expulsion, hydrocarbon accumulation and preservation process in the Lower Paleozoic Sinian-Cambrian source rocks were clarified.