Through the methods of polarizing microscope and cathodoluminescence, the diagenesis of Late Carboniferous phylloid algal reefs in southern Guizhou is studied, which indicates diagenesis are mainly of bio-binding and baffling actions, micritization, cementation, compaction-pressure solution, fracture, recrystallization and dissolution in type. Based on thin section analysis and cathodoluminescence, the diagenesis can be subdivided into four stages, including quasi-contemporaneous diagenesis phases, early diagenesis phase, burial diagenesis phase and epigenetic diagenesis phases. Diagenetic and cathodoluminescent characteristics show that the reefs have gone through marine, meteoric freshwater and buried diagenetic environment.