The pollen morphology of 63 species, one subspecies and six varieties of 11 genera in the family Liliaceae was studied in detail using light microscopy (LM) and scanning electron microscopy (SEM). Among them, 22 species and one variety are reported for the first time. Ten pollen characteristics (shape in polar view, ends in polar view, width of colpus, depth of colpus, length of colpus, colpus costa, colpus membranes, type of surface ornamentation, muri, lumina) were selected for cluster analysis of the genera Gagea and Lloydia and for cluster analysis and principal component analysis of the genera Lilium and Nomocharis. The results show that the polar view, colpus morphology and surface ornamentation of pollen grains have important systematic significance. The surface ornamentation of pollen grains in this study can be divided into five types, namely gemmate, reticulate, rugulate, rugulate-perforate and verrucate. In combination with the results of previous research, our results suggest that (i) Clintonia and Streptopus should be included in the family Liliaceae; (ii) Fritillaria and Lilium should be considered independent genera; (iii) Lloydia should belong to Gagea; and (iv) Nomocharis should be merged into Lilium. But our results do not support dividing Lilium into seven sections.