Objective   To analyze the time variation of gender size difference rates of human mandibles in Holocene, and to explore the change rates of the mandible sizes of males and females among different time periods. Methods  Using 520 mandibles from several archaeological sites in China, we used SPSS 18.0 to compare the metric traits between the male and female in the same and different time periods, by independent sample t test, and calculate the gender difference rates and the change rates among different time periods. Results  The sizes of male mental foramen and mandibular foramen in present mandibles were bigger than that in Neolithic and Bronze-Iron Age, while the difference of the female among different time periods was not significant. The gender difference rate of the size of mental foramen and mandibular foramen was bigger in present than that in Neolithic and Bronze-Iron Age. Conclusion  The gender difference rates in mandible are greater in recent population than that in Neolithic and Bronze-Iron age. The comparison of cross section perimeter ratio indicates that the robust of mandible body at mandibular first molar(M1) declines compared with that at mandibular first premolar(P3) in Holocene. The position of mental foramen became higher during Neolithic to present.