Large amounts of pyrites frequently found in Lower Paleozoic (especially in Ordovician) carbonates of the Tarim Basin occur in carbonate, fractures, dissolution pores, karst breccias or cave fillings of sand and mud clasts. The pyrites are present as dispersed grains with sizes up to several millimeters. Studies of the extensively existent pyrites not only can determine the process of the associated fluids but also are of great significance in discussing the origin of the extensively-concerned high concentration of H2S in natural gas within the Ordovician carbonates. In this paper, the modes of occurrence of the pyrites were described in detail and the sulfur isotope composition was analyzed. 18 pyrite samples for sulfur isotope analysis were collected from cores of different wells, among which 13 are located in the Tabei uplift, and 5 in the Tazhong uplift. According to the modes of occurrence and sulfur isotope composition, the pyrites can be divided into two groups. The first group occurs in karst breccias or in sand and mud clasts and is thought to be associated with surface meteoric karstification. The δ34S values of the first group range from -25.7‰ to -4.7‰, -17.6‰ on average. According to modes of occurrence and sulfur isotope composition, the first group is probably a product of bacterial sulfate reduction (BSR). It is thought that the BSR might have taken place under the condition of relatively low temperature when the carbonate was uplifted to surface or subsurface and altered by meteoric waters. The second group of pyrites principally occur in fractures of carbonates and are sometimes coexistent with calcite veins where the homogenization temperature of the fluid inclusions is relatively high. The values of the second group range from +11.2‰ to 31.3‰, 21.8‰ on average. The modes of occurrence and sulfur isotope composition show that the second group might be a product of thermochemical sulfate reduction (TSR). The TSR is considered to have taken place under a condition of relatively high temperature in association with magmatic activities. The sulfur involved in both BSR and TSR is thought to have originated from anhydrite or sulfate in the formation water which was extensively existent in Cambrian, Ordovician and Carboniferous strata. High concentration of H2S was found in the Ordovician carbonate which contains large amounts of pyrites. For instance, the measured concentration of H2S is up to 102908.17 mg/m3 in the natural gas produced from the Ordovician carbonate of the T740 well which is located in the main area of the Tahe oilfield in the Tabei uplift. The area with high concentration of H2S is also the area with extensive magmatic activity. According to sulfur isotope composition and its relation with the distribution of igneous rocks, the high concentration of H2S in the natural gas in Lower Paleozoic carbonates of the Tarim Basin is considered to be predominately the product of TSR.