Bedded sulfide orebodies occur in the Wushan and Dongguashan Cu deposits in the Middle and Lower Yangtze River mineralization belt. In this study, we found many typical circular or laminated textures in the bedded sulfide ores. Based on microscopic observation of thin sections of the ore samples, carbon and oxygen isotopic analysis, and scanning electron microscope (SEM) observation, we suggested that this type of sulfide ores belongs to a mineralized kind of carbonate mud mound. The macroscopic structures of these sulfide ores are quite similar to those of cavities system of typical carbonate mud mounds, and there are also bacteria structures found in some of the ore samples with SEM analysis. The conservation conditions of the carbonate mud mounds in the two copper deposits are different, in the Dongguashan Cu deposit, a lot of primary exhalative sedimentary textures are preserved, bacteria structures are found, and the carbon-oxygen isotopic compositions show primary sedimentary characteristics, while those in the Wushan Cu deposit show hydrothermal altered/overprinted textures, and no bacteria structures have been found so far, the carbon-oxgen isotopic compositions also indicate a hydrothermal reworking. In summary, the discoveries of carbonate mud mounds structure sulfide ores in the Wushan and Dongguashan Cu deposits provide new evidence for the Hercynian sedimentary exhalative mineralization in the Middle and Lower Yangtze River mineralization belt.