Ornithogalum caudatum Ait exhibits strong physiological adaptability; however, it suffers a serious menace of pollen abortion, as almost no seed is formed in the plants. In the current study, chromosome karyotype of root-tip cells (RTC) during mitosis, and chromosome behavior of pollen mother cells (PMC) during meiosis in O. caudatum were investigated. We recorded 18 euchromosomes with variable number (28~36) of B chromosomes in the somatic cells genome. In leptonema of meiotic prophase I, the synapsis between euchromosomes was normal, but there were several darker granular nodular bodies in the cells, which could be the precursor for B chromosomes. Some of the cells were observed as duplication loop in zygotene, indicating that the PMCs had gone through a chromosome structure variation with duplication, which could reduce the fertility of pollens. Numerous chromosome bridges, fragments and lagged chromosomes were observed in meiosis anaphase I. It reflects that these cells might have undergone paracentric inversion, which is one of the important reasons of pollen abortion. In meiosis anaphase II, the sister chromatids separate unusually forming the triad, which leads to gamete sterility. These findings conclude that pollen abortion in O. caudatum mainly results from the variation in chromosome structure, which could be related to the B chromosomes in somatic cells.