The low fertility of naked seed rice (NSR) was investigated by the following observations: somatic chromosome constitute, behavior of pollen mother cells (PMCs), the germination of mature pollen grains, the development of male and female gametes and the structure of the anther opening. The results indicated that somatic chromosomal number was 2n = 24, behavior of PMCs were normal and most of pollen grains could regularly develop further to mature male gametophytes in NSR. And dehiscence chamber and thickened endothecium cell (TEC) in numerous anthers of the NSR were developed abnormally after dicaryotic phase, result in few anthers complete opening and most partly opening or failure to opening, therefore much fewer of pollen grains attach on the stigma as compared with normal variety. Furthermore most of embryo sacs possessed abnormal structure and were sterile. All of above illustrated that the failure of the anther opening and the abortion of female gametophyte were main factors controlling the low seed-setting rate of the NSR.