The aim of this study was to understand the relationship between pollen mother cells meiotic characteristics and pollen fertility of Houttuynia cordata Thunb. The meiotic process of pollen mother cell was observed by carbol fuchsin staining in two populations of H. cordata, and pollen fertility was determined by triphenyl tetrazolium chloride staining (TTC), I₂KI staining, BK medium culture method, and fluorescence microscopy observation, respectively. The results showed that: (1) the meiosis processes were closely correlated with the inflorescence size, anther color and length. (2) About 88.2% of the pollen mother cell meiosis are normal, 11.8% of the pollen mother cell meiosis abnormalities. (3) Some abnormal division had been observed at pollen mother cells meiosis process, such as occurrence of micronuclei, lagging chromosomes, chromosome bridges, unequal segregation, and polyads. Cytomixis occurred in pollen mother cells at dyad of the meiosis stage and mononuclear pollen development process. (4) The pollen viability of the two populations was not more than 1.5%, and the pollen was hardly germinated. We suggested that the main reason of low pollen fertility was that the uninuclear pollen development process rather than the abnormal division of pollen mother cell meiosis in H. cordata. The pollen vitality was no more than 1.5%, and the pollen was almost germinated.