Organic-mineral interactions are universal in natural environments. They cause the majority of the total organic carbon (TOC) in sediments and sedimentary rocks to combine with clay minerals to form organo-clay composites. However, the role of organo-clay composites in hydrocarbon generation is not clear. In this study, we select a suite of successively deposited shales to examine the association between organic matter (OM) and minerals, and to analyze the correlations of TOC with different mineral surface areas (MSAs) and the Rock-Eval pyrolysis in both bulk shales and their organo-clay composites. We find that OM in shale is dominantly incorporated with clay minerals by the main way of adsorbing on internal mineral surfaces rather than external mineral surfaces, which forms organo-clay composites. Further analyses on TOC-MSA correlations demonstrate the great heterogeneity of OM occurrence within shale. Also, the OM quality of organo-clay composites is poorer for hydrocarbon generation than that of bulk shales. We conclude that the variations in organic geochemistry between bulk shales and organo-clay composites are caused by hydrocarbon generation, which reduces the OM quality for further generation. Taken together, organo-clay composites dominate OM occurrence and have been generating hydrocarbons, which highlight the main control of organo-clay composites on hydrocarbon generation in natural samples. In comparison with the long-standing theory of hydrocarbon generated from kerogen, we propose the organo-clay composites to be the in situ and main source for hydrocarbon generation. This new hypothesis improves the existing knowledge of the organic origin of hydrocarbons in natural systems.