A set of organic-rich shales developed in the lower part of the Lower Silurian Gaojiabian Formation in the Lower Yangtze region, South China. The paleoenvironment and the organic matter (OM) accumulation mechanism in the Lower Yangtze region are rarely studied, restricting the in-depth understanding of the shale gas exploration prospects of this region. This study described the petrological, mineralogical characteristics and geochemical properties of the organic-rich shales of the Gaojiabian Formation in the Lower Yangtze region (Well TD2) using multidisciplinary approaches. The purpose is to study the palaeoenvironment evolution of organic rich shales, and reveal the controlling factors and accumulation mechanism of OM. Two shale sections with high TOC content developing in the lower part of the Gaojiabian Formation were identified through petrological observations and geochemical analysis, namely the lower shale section (LSS) and the upper shale section (USS) with TOC content of 0.79–4.62% and 0.65–2.92%, respectively. The two organic-rich shale sections were formed in a suboxic-anoxic environment. The Cd/Mo, Co × Mn, Mo/TOC values show that the USS and the LSS were formed in a strongly restricted water environment and were not affected by upwelling, and the environment of the USS was more restricted than that of the LSS. The paleoproductivity proxies indicate the two sections have a high-productivity background, and that the LSS has a higher paleoproductivity level than the USS. The terrigenous input shows a long-term growth trend. Compared with the LSS, the USS had more terrigenous input and was closer to the source area. The chemical index of alteration (CIA) indicates that the shale was formed in a warm and humid climate. The index of compositional variability (ICV) shows that the USS has a more mature composition than the LSS and was likely dominated by recycling. The relationships between TOC content and several geochemical proxies indicate that the OM accumulation was mainly controlled by redox condition, paleoproductivity and terrigenous input, whereas these three factors are determined by the combined impact of the sea level and regional tectonic movement. On this basis, this study reconstructed the paleoenvironment and the OM accumulation model. The OM accumulation of the LSS was mainly controlled by relatively high regional sea level affected by global transgression, the anoxic-suboxic water environment, the high paleoproductivity, and a small quantity of terrigenous input, while the OM accumulation of the USS was primarily controlled by the suboxic condition affected by decreased relative sea level resulting from the strengthened regional tectonic movement, the relatively weakened paleoproductivity, and the increased recycled terrigenous input. The above understanding provides important enlightenment for deepening the study of OM enrichment and shale gas exploration direction of the Gaojiabian Formation in the Lower Yangtze region.