In this study, three photo-thermo-sensitive genic male sterile(PTGMS) lines and four cytoplasmic-nuclear male sterile (CMS) lines were used as materials to investigate the embryo sacs fertility and outcrossing seed setting rate. Three PTGMS lines were W7415S, AnnongS and Peiai 64S. Four CMS lines were Zhenshan 97A with wild abortion male sterile cytoplasm, Zhenshan 97A with Yegong male sterile cytoplasm, HuanongA with wild abortion male sterile cytoplasm and HuanongA with Yegong male sterile cytoplasm. The results showed that the embryo sac fertility of the male sterile lines was positively correlated with their outcrossing seed setting rate. For the PTGMS lines, the embryo sac fertility was affected by the heredity, environment and their interaction, and the embryo sac fertility at sterile period was lower than that at fertile period. The embryo sac fertility of the PTGMS lines at fertile period was close to that of the CMS lines in the early season. For the CMS lines, the embryo sac fertility was mainly affected by the environment, and the embryo sac fertility in the early season was lower than that in the late season. Furthermore, the embryo sac of PTGMS lines was more sensitive to the environment than that of CMS lines, especially W7415S. In conclusion, the embryo sac fertility is an important factor affecting the outcrossing seed setting of male sterile lines in rice, and embryo sacs fertility is affected by photoperiod and temperature in some PTGMS lines. The effect of embryo sac fertility should be considered in the breeding of male sterile lines in rice.