The aim of this study is to investigate molecular organic geochemical characteristics of the Lower Palaeozoic carbonate rocks by analyzing carbonate rocks from some drills in the buried hill zones such as Chegu, Yigu and Zhuanggu in the Jiyang depression. The results show the biomarker distributions and carbon isotopic compositions of bitumen A from these Lower Palaeozoic carbonate rocks, and they can be used to identify potential indigenous oils and gases in the Lower Palaeozoic of the Bohai Bay area. In addition, the study also indicates that the n-alkane fractions of crystal-enclosed organic matter in carbonate rocks have obvious different distributions and carbon isotopic compositions from those in bitumen A. The main characteristics of the early organic matter are still reserved in crystal-enclosed organic matter, so they can be used for discussing the paleoenvironment.