Extensive organic-matter (OM) rich facies (black shales) occur in the Ordo-Silurian boundary successions in the Yangtze area, South China. To investigate the redox changes of the Yangtze Sea during the Ordo-Silurian transition, two OM sections (Wangjiawan in Yichang, Hubei Province, and Sanjiaguan in Zhangjiajie, Hunan Province) straddling the Ordo-Silurian boundary are studied. The measurements finished in this study include contents of the total organic carbon (TOC), pyrite sulphur, and different species of Fe, including dithionite-extractable Fe (FeD), pyrite Fe (FeP), HCl-extractable Fe (FeH), and total Fe (FeT), in black shales, as well as other redox proxies, such as the S/C ratio, the ratio between highly reactive Fe (FeHR = FeD + FeP) and FeT, and the FeP/(FeP + FeH) ratio, known as the degree of pyritization (DOP). In the Wangjiawan section, the Middle Ashgill sediments have high FeHR/FeT ratios (0.20–0.77; avg. 0.45), high DOP values (0.21–0.72; avg. 0.54), and a relatively constant sulfur content independent of the organic carbon content. By the contrast, the mid-early Hirnantian deposits generally have low FeHR/FeT ratios (0.10–0.35; avg. 0.21), low DOP values (0.11–0.40; avg. 0.28), and S/C values are clustering on the normal marine value (S/C = 0.36). The late Hirnantian and early Rhuddanian deposits, similar to those of the Middle Ashgill deposits, are characterized by high FeHR/FeT ratios (0.32–0.49; avg. 0.41), high DOP values (0.46–0.68; avg. 0.53) and fairly constant sulfur contents. These data suggest the occurrences of marine anoxia on the Yangtze Sea shelf during intervals of the Mid Ashgill, Late Hirnantian and Early Rhuddanian, and ventilated and oxygenated marine conditions during the mid-early Hirnantian time. The mid-early Hirnantian ventilated event was concomitant with the global glacial period, likely resulted from the glacio-eustatic sea-level fall and subsequent circulation of cold, dense oxygenated waters upon the shelf seabed. Accordingly, the abrupt change from oxygenated to anoxic marine waters from the late Hirnantian and the early Rhuddanian were resulted from the post-glacial rise of eustatic sea level. Combined with the data from Sanjiaguan section near the subemergent highland, salinity stratification of water columns are strongly evidenced by very low S/C ratios ( 0.00–0.08, avg. 0.02), low FeHR/FeT ratios (0.10–0.37, avg. 0.27), low DOP values (0.01–0.27, avg. 0.10), and TOC contents (0.72%–4.27%, avg. 2.55%). Under this circumstance, the anoxic water columns could have formed beneath the halocline, above which desalinized waters formed. In the Wangjiawan section, TOC contents are generally high (0.94–9.32%, avg. 4.44%), but low (0.35%–2.12%, avg. 1.29%) in the mid-early Hirnantian that is coincident with the oceanic oxic stage, together with relation of the organic contents to the stratal thickness, suggesting that the accumulation of the organic matter was mainly controlled by the oxygen levels of the water columns; on the other hand, productivity and depositional rate may also have played a role in the organic accumulation and preservation.