Limestone-marl alternations (abbr. LMAs) is a good target to trace high precision cyclostratigraphy by orbital-forcing; however, their origin (primary vs. diagenetic) is still controversial, and thus the application of LMAs were limited in ancient geological records. In this study, we investigated widespread Permian LMAs of various depositional circumstances in South China by multiple analyses of traditional petrography, mineralogy, major elements (Al2O3 vs.TiO2), and novel trace and rare earth element (REE) geochemistry performed by solution-based and in situ technologies. Original depositional difference at limestone and coupled marl beds was identified in light of the high volume of siliciclastic components in marls, no differential compaction, diverse element (and its oxide) concentrations of Al2O3, Zr, Th, and REE, and flattened but inconsistent shale-normalized REE patterns. Diagenesis-dominant LMAs are typical of significant compaction of fossils and rare aragonite skeletons as well as a large number of diagenetic clays (sepiolite and talc) preserved in marl beds. They are also shown as similar shale-normalized REE patterns in coupled limestone and marl beds, and weak siliciclastic contents of Al2O3, Th, Zr and REE. It is noted that original carbonate sedimentation can also form LMA in diagenetic process evidenced by two nearly fully consistent seawater-like REE patterns with diagnostic positive La and negative Ce anomalies, superchondritic Y/Ho, and clear light REE depletion relative to high REEs. Diagenetic LMAs with weak but identical terrigenous supply at limestone and marl beds can also be identified, but the role of diagenesis is difficult to be distinguished within LMAs when the volumes of siliciclastics were inconsistent during their original deposition. Therefore, the widely-distributed LMAs in shallow marine environments with limited siliciclastic input (especially pure carbonate LMAs) need to be caution in the application of cyclostratigraphy, and related astrochronology and magnetostratigraphy, which are based on stable and primary depositional thickness, component construction, and geochemical signatures.