The development of high-quality carbonate hydrocarbon reservoirs in the ultra-deep (7000–10000 m) Lower Paleozoic strata of the Tarim Basin was substantially related to tectonic evolution, strike-slip faults, and diagenetic fluids. Detailed studies of the influences of tectonic evolution and strike-slip faults on the properties of diagenetic fluids and the development mechanisms of ultradeep carbonate reservoirs under the control of both faults and fluids are required to identify high quality reservoirs. In this study, end-member geochemical indicators of meteoric water, hydrothermal fluid, and formation fluid were constructed based on typical diagenetic mineral and geochemical data obtained from representative wells. Meteoric karst associated with strong tectonic uplift was the main diagenetic event along strike-slip faults in the Tahe area. The Shunbei area was generally affected by buried formation water, and locally by weak meteoric water or hydrothermal fluids. The Tazhong, Shunnan, and Gucheng areas were predominantly affected by strong hydrothermal fluids along strike-slip faults associated with strong volcanic activity, while some wells, such as TZ12, reveal the influence of thermochemical sulfate reduction (TSR). Differences in fault fluid types and properties resulted in differential development of ultra-deep carbonate reservoirs among the different areas. In the Tahe area, meteoric water alteration along faults formed karst fracture-cavity reservoirs. In the Shunbei area, fault-cavity carbonate reservoirs were formed by strong strike-slip faults, whereas fluid alteration was weak. Hydrothermal dissolution reservoir in the Tazhong area, hydrothermal silicification reservoir in the Shunnan area, and hydrothermal dolomitization reservoir in the Gucheng area are developed, respectively.