With a detailed study on petrology, mineralogy and geochemistry of some important Ordovician carbonate well core samples in Tazhong uplift of Tarim Basin, the distinguishing symbols of hydrothermal karstification are first put forward as the phenomena of rock hot depigmentation, hot cataclasm and the appearance of typical hydrothermal minerals such as fluorite, barite, pyrite, quartz and sphalerite. The main homogenization temperatures of primary fluid inclusions in fluorite are from 260 to 310°C, indicating the temperature of hydrothermal fluid. The fluid affected the dissolved rocks and showed typical geochemistry features with low contents of Na and Mg, and high contents of Fe, Mn and Si. The ratio of 3He/4He is 0.02Ra, indicating the fluid from the typical continental crust. The hydrothermal fluid karstification pattern may be described as follows: the hot fluid is from the Permian magma, containing dissolving ingredients of CO2 and H2S, and shifts along fault, ruptures and unconformity, and dissolves the surrounding carbonates while it flows. The mechanism of hydrothermal karstification is that the mixture of two or more fluids, which have different ion intensity and pH values, becomes a new unsaturated fluid to carbonates. The hydrothermal karstification is an important process to form hypo-dissolved pinholes in Ordovician carbonates of Tazhong uplift of Tarim Basin, and the forming of hydrothermal minerals also has favorable influence on carbonate reservoirs.