The evolutional process of palaeoceanic environment and its effect on the accumulation of organic matter during the Ordovician–Silurian transition in Lower Yangtze region has been overlooked compared to that in Upper Yangtze region of South China, although their paleogeographic settings were expected to be discrepant. This paper documents the marine depositional environment, paleoclimate, and sediment supply changes, and discusses their roles in controlling the organic matter enrichment in sedimentary rocks within the Ordovician–Silurian transition of the Lower Yangtze region, using the latest geochemical data of the continuous drilling core. The stratigraphic framework of the Ordovician–Silurian transition in the Lower Yangtze region is composed of two third-order sequences, each of which can be subdivided into a lower TST (transgressive systems tract) and an upper RST (regressive systems tract). TST1 represented an evident depositional transition stage which was marked by the ending of the underlying carbonate sediments and the initiation of the terrigenous clastic-dominated sediments. Geochemical proxies indicate that the relatively low productivity, dysoxic water column condition, and high sediment supply flux collectively resulted in inadequate organic matter hosted in deposits of the TST1. During the depositional period of RST1, the global sea level declined due to the Hirnantian glaciation age. The icehouse also caused the decrease in overall river flux and, thus, the terrigenous clastic sediment supply. The icehouse also strengthened the upwelling that occurred in the Lower Yangtze sea. The upwelling boosted the marine algae explosion through the delivery of abundant nutrients, which not only enhanced paleoproductivity but also led to an anoxic environment by oxygen consumption. Such high paleoproductivity, anoxic water column environment, and low sediment supply flux caused the deposition of organic-rich shale. The sea level rose during the TST2 due to the ending of an ice age. The relatively large water depth and high paleoproductivity associated with volcanic eruptions are the main factors that caused the enrichment of organic matter during this stage. During the deposition of RTS2, the increase of sediment supply flux resulted in a decrease in accommodation space and water depth and the dilution of organic matter in deposits, which was the primary constraint of organic matter accumulation.