Cytoplasmic male sterility (CMS) is a widespread phenomenon in higher plants and has been applied in the commercial production of hybrid seeds. Two CMS lines A1 and A2 of maize were obtained previously by a transgenic experiment. In this study, we conducted cytological observation of developmental microspores with CMS line A1, A2 and their maintainer line (18 red) using paraffin section technology. We also analyzed DNA methylation levels at different developmental stages using high performance liquid chromatography (HPLC). Our results showed that the pollen abortion of A1 and A2 mainly happened from the tetrad stage to the middle of mononuclear stage. Another abortive phenomenon found in CMS line A2 occurred at the pollen mother cell stage. The DNA methylation level of leaf increased rapidly from the seedling stage to the shooting stage in 18 red, while it remained constant in A1 and A2. For the tassel, the DNA methylation levels in 18 red increased gradually during the anther development, while a peak of DNA methylation level occurred in A1 and A2 at the tetrad stage, corresponding to the abortion period of microspore. This result suggested that the level of DNA methylation in the tassels is associated with the pollen abortion characteristics in CMS lines. In summary, our results implied a connection between pollen abortion and epigenetic regulation in maize CMS.