Intensive igneous activities took place in the Tarim Basin in the Permian. Hydrothermal fluids were derived from igneous activities, migrated along faults and fractures and reacted with carbonate host rocks. When carbonates are dissolved by hydrothermal fluids, some mineral assemblages, typical of hydrothermal genesis, would precipitate from the hydrothermal fluids. The mineral assemblages include (1) fluorite-quartz, (2) sphalerite-chlorite-calcite and (3) barite-quartz-pyrite-siderite assemblages. The carbonates are relatively enriched in Fe, Mn and Si, where the carbonates were partially dissolved by hydrothermal fluids. Under the influence of hydrothermal fluids, numerous dissolution pores of few millimeter were created, and consequently the porosity and permeability of carbonate reservoir beds were significantly enhanced. The enhancement in porosity and permeability is very important for carbonates to be efficient oil and gas reservoir beds, particularly for those that have not experienced subaerial karst.