Limestone—marl alternations, including the entire spectrum from nodular alternations to well bedded sequences, widely distributed from shallow shelf to pelagic realm, are usually interpreted to reflect palaeoenvironmental signals in a high resolution. Despite the long lasting research history on limestone—marl alternations, it is still controversial if these alternations reflect environmental changes or are produced by pure diagenetic process. Some scholar believe that the diagenetic process only enhances the differences of primary signals, while others propose that pure diagenesis can not only alter the original records but also produce the same phenomenon as primary deposits. Differential diagenesis in limestone—marl alternations includes redistribution of calcium carbonate from marl layers to limestone beds by dissolution, migration of ions, and reprecipitation. Aragonite in marl layers was dissolved to cement limestone, which took place in shallow burial realm. Thenceforth, mechanical compaction and then pressure dissolution were concentrated in the less cemented strata. The dissolution of aragonite in the shallow marine burial realm is thought to have been initiated by modification of the pore water chemistry by bacterial oxidation of organic matter. This article reviews the environment and the process of differential diagenesis, discusses the related question, including the source of the cements and the role of organic matter during early diagenesis. At last, the Qixia Formation is selected as an example to explain the origin of those alternations.