Cohesin is a multi-subunit protein responsible for holding sister chromatids together during mitosis and meiosis. Each subunit is functionally essential, and their deletion is always lethal. SCC3 is a highly conserved constituent of the cohesin complex. However, the exact mitotic and meiotic functions of SCC3 in rice remains to be elucidated. Here, we found null alleles of SCC3 cause embryo lethality. Only scc3 weak mutants could survive and show vegetative and reproductive defects. Specifically, the replication process of sister chromatids is disturbed in scc3 during interphase both in mitosis and meiosis. Moreover, SCC3 has distinct localization patterns between mitotic and meiotic cells. The numbers of DMC1, RAD51 and ZIP4 foci are significantly decreased in scc3, and ZEP1 displays as an abnormal punctate foci during zygotene. Importantly, the scc3 fails to synapse, but in this case chromosome fragmentation is absent. Thus, SCC3 seems to inhibit inter-sister chromatids repair (ISR), and this process is independent of DMC1-mediated ISR.