The mature embryo sac fertility, formation and development of embryo sac of 141 accessions of O. rufipogon Griff. collected from the six sampling sites in Gaozhou, Guangdong Province were studied by using the technology of whole-mount stain-clearing confocal laser scanning microscopy (WCLSM). The results showed that some abnormal phenomena to different extent, such as abnormal embryo sac with non-female germ unit, abnormal embryo sac with polar nuclei in position, abnormal embryo sac with polar nuclei in number and embryo sac abortion, etc., were found in mature embryo sac. Those abnormal embryo sacs having abnormal fertility dued to no normal eggs, which caused seed setting rate to drop. The mean percentage of abnormal embryo sac of all the 141 accessions was 11.11% and the highest one was 67.86%. Development of wide rice in Gaozhou was similar to that of O. sativa L., which belongs to the Polygonum type. Abnormal phenomena in different periods of embryo sac development, including degeneration of megaspore, embryo sac abnormality during the periods of two to eight nucleate etc., were found in the plants with low seed setting rate. Few pollens were found on the stigma of 69 accessions observed after pollination, which would cause low percentage of fertilization. It was considered that a few of pollen grains on the stigma was one of the main reasons making seed setting rate decrease. The comprehensive factors resulting in the low seed setting rate of wide rice in Gaozhou were discussed in this paper.