To elucidate the morphological diversity and genetic characteristics of the pollen of Polygonatum species, this study utilized a total of 46 samples encompassing six species and one variety of Polygonatum. Scanning electron microscopy (SEM) was employed to examine the morphological traits of the pollen and to analyze the evolutionary patterns and genetic relationships among Polygonatum species. The results indicate that the pollen grains of the 46 Polygonatum germplasm are uniformly characterized as monads, heteropolar, bilaterally symmetrical, atreme, and possess a mono-sulcus. They were peroblate (P/E-ratio = 0.36–0.42) in shape and medium to large (P = 18.17–27.15 μm, E = 44.11–67.07 μm) in size. And there are four types of exine ornamentation: reticulate, reticulate–perforate, reticulate–rugulate, and reticulate–verrucate. The 46 germplasm resources were classified into four clusters based on the results of a pollen morphology clustering analysis: P. cyrtonema and P. macropodum were grouped into cluster I, P. filipes and P. odoratum into cluster II, P. kingianum and P. kingianum var. grandifolium into cluster III, and P. alternicirrhosum was classified as cluster IV, standing alone. This study tentatively suggests that pollen morphology, particularly pollen size and exine ornamentation, can serve as a valuable reference for the classification, genetic relationship, and evolutionary patterns of the genus Polygonatum.