Lilium lancifolium (syn. L. tigrinum) is the only polyploidy-complex species involving both diploid (2n = 2x = 24) and triploid (2n = 3x = 36) plants in the genus. The origin of natural triploid remains a mystery and research has been limited mainly to chromosomal studies that have overlooked research on pollen ontogeny. By spatiotemporal comparison of the development and morphology of diploid and triploid pollen grains, we study the correlations between pollen fertility and morphological development in diploid and triploid plants and propose the necessity and importance of further research on natural polyploid-ontogenetic diversity. In this comparative investigation, we used various microscopy techniques including histological analyses, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The main morphological differences between triploid and diploid pollen grains started with abnormal tetrad formation of triploid, followed by inadequate amylogenesis and amylolysis in young microspores, and finished with the formation of an abnormal structure of pollen surface layers in maturing pollen grains, which finally resulted in pollen grain unfolding and male sterility. From observing the series of morphological events that induced male-sterile pathway in natural triploid pollens, this study showed a variety of correlations between pollen development and fertility, which differed from male sterility resulting from gene mutation, indicating that there exists greater variability in pollen male-sterile ontogeny. Our results suggest that multilateral research is required for understanding the fickle ontogeny of natural male-sterile polyploid.