Abstract: For the genetic analysis of minor effect restoring gene in rice, the CMS lines of Zhenshan 97A, Longtepu A and Jinfu 1A with different fertile levels were used as materials to investigate three sterility indexes, bagged seed setting rate, dark pollen rate by I2-IK dyed and rate of florets with fertile anthers.The results showed that the appearance of abnormal plants in CMS-WA was due to partial restoration of self-fertility few floras caused by minor effect restoring gene.Adopted the method of genetic improvement could eliminate part of minor effect restoring gene to get purification and elimination, but not completely ruled out.This index of rate of florets with fertile anthers could be use as a suitable tool to study heredity laws of minor effect restoring genes and its further molecular mechanism.