We have evaluated the existence of good paleo-carbonate reservoirs in fault damage zones with a burial depth exceeding 5800 m in the Central Paleo-Uplift, Sichuan Basin, China. The relationships between fault system and sedimentation, and the formation of the paleo-carbonate reservoirs have been explored, which have long been ignored by previous studies due to the low-quality seismic data and the prevalent assumption of weak tectonic movement. Data from different sources such as newly acquired and processed seismic data, cores, and well-logs are used to study the characteristics and origin of the fault system and their controls on the formation of paleo-carbonate reservoirs. The main findings are as follows: (1) The Sinian-Permian fault system in the study area mainly comprises strike-slip faults with different scales plus a small number of locally developed collapse-related concentric faults. (2) The Sinian-Permian fault system, which usually has normal throw, mainly developed in an extensional stress field and its evolution spanned five stages including the basement-fault formation stage in the Yangtze cycle, extensional dextral strike-slip faults formation stage in the Xingkai cycle, weakly compressional sinistral strike-slip faults formation stage in the Caledonian cycle, extensional faults formation stage in the Hercynian cycle, and compressional transformation stage in the Indosinian-Himalayan cycles. Most faults formed in the Xingkai and Caledonian cycles, whereas the Indosinian-Himalayan cycles had a weak effect on the Sinian-Permian fault system in the study area. (3) Different types of faults have different effects on the sedimentation, formation, and preservation of the paleo-carbonate reservoirs. The synsedimentary faults provide necessary tectonic background for the sedimentation of high-energy facies, whereas the successive faults and coalesced fractures determine the formation, distribution, and preservation of the porous karst carbonate reservoirs. The basement faults controlling the hydrothermal fluids only cause partial filling of the existing pore spaces; thus, most pore spaces in the karst carbonate reservoirs are able to be preserved. Therefore, the fault damage zones within the paleo-carbonate strata produce good reservoirs and important exploration targets.