Abstract The Upper Ordovician–Lower Silurian mudstones (including the Wufeng, Guanyinqiao and Longmaxi Formations) in the Sichuan Basin are some of the most important shale gas plays in China. In order to enhance our understanding of the process of formation of organic carbon up to 10%, optical, microscopy and geochemical methods have been used to investigate the petrographic and geochemical characteristics of the formation. Firstly, three mudstone lithofacies were identified based on a wide variety of mudstone laminations. These are: (a) indistinctly laminated mudstone; (b) parallel-laminated mudstone; and (c) nonparallel-laminated mudstone. Then, combining with the evidence from depocenter migration, Th/U ratios and total organic carbon, the abundant organo-minerallic fabrics suggest that organic carbon was preferentially deposited and preserved in anoxic, low energy and stagnant water conditions during deposition of the Wufeng and Longmaxi Formations. On the contrary, the Guanyinqiao Formation with poor organic carbon was deposited in oxic and high-energy water conditions.