The shelf-like protuberance on the outer side of the pit in polygnathid conodonts is a unique and easily recognizable feature usually viewed as taxonomically significant for the biostratigraphically important species Polygnathus serotinus. However, the protuberance is also developed in other late Emsian-early Eifelian polygnathids, which mainly include P. praeinversus, P. vigirei, P. pseudoserotinus and P. linguiformis bultyncki. Although several evolutionary lineages have been proposed to elucidate the phylogenesis of the protuberance, its morphogenesis has been rarely studied. In this study, intraspecific variation of P. linguiformis bultyncki is investigated on the basis of abundant specimens from South China and Germany, and two morphotypes are recognized. Moreover, three morphogenetic patterns of the shelf-like protuberance are proposed. Polygnathus praeinversus and P. pseudoserotinus are assigned to the first morphogenetic pattern, with the protuberance formed as a vestigial outer flank of the asymmetrical basal cavity. The second pattern, which can be applied to P. serotinus and P. vigirei, is characterized by a protuberance that is formed as a shelf-like extension of the pit partially buttressed by platform material in juvenile/immature specimens, and by a well-developed shelf-like extension of the pit on its inner side and a bulge in the platform proper on its outer side in mature specimens. Polygnathus linguiformis bultyncki is characterized by the third morphogenetic pattern. Its protuberance is ontogenetically acquired and though absent in juvenile specimens, in immature and mature specimens it is formed as a bulge in the platform proper fully supported by platform material. This study provides an exemplar for conodont research of other geological periods as growth histology can play an important role in investigating morphological variation of conodonts.