The controlling mechanisms for the accumulation and preservation of organic matter in residual bay environments during the transition from marine to continental settings are not well understood, although oil gas source rocks can form in this setting. In this study, we develop a case study for the Early Cretaceous black rock series in the northern Qangtang Basin, Tibet (i.e., the Upper Member of the Suowa Formation), by conducting a combined organic and inorganic geochemical analysis of micritic limestone, marl, and shale samples from an outcrop section. Results show that total organic carbon (TOC) contents of the studied samples are between 1.74% and 7.71%, with the organic matter being Type II/III kerogen. Of the three factors that could influence the observed TOCs and organic matter types, including paleoproductivity, preservational environment, and sedimentation rate, the preservational environment appears to be the dominant factor, independent of lithology. This is typically supported by the relatively modest covariance between redox-sensitive parameters and TOC contents, e.g., R-2 = 0.625 in the Mn/Ca-TOC diagram and R-2 = 0.690 in the U/Th-TOC diagram. This suggests that the suboxic anoxic environment in the lagoon at the residual bay area promoted favorable conditions for organic matter preservation. In contrast, the other two factors, i.e., paleoproductivity and the rate of sedimentation, differed between three types of lithologies. For shales and micritic limestones, the effect of paleoproductivity was limited on the abundance of organic matter, and no significant effect of sedimentation rate was detected. In contrast, the paleoproductivity has a definite effect on the amount of organic matter preserved in the marls. These findings also add to our knowledge of the depositional environment that existed during the Early Cretaceous marine continental transition in the Qiangtang Basin and further built our understanding of the potential hydrocarbon resources of the basin.