Abstract: Flat pod reduces the number of seeds per plant and thus causes yield loss in soybean. However, its characteristic and genetic mechanism are still unclear at present. Therefore, in this study, the characteristics of flat pod rate(FPR) among 1554 soybean accessions over three years were identified, and the related genetic loci controlling FPR were mapped by genome-wide association study(GWAS). The results showed that environments(years), genotypes and the interaction between them all have a significant effect on FPR. The range of FPR was from 0.00% to 70.30% with a mean of 4.30%. 75% of the accessions had FPR less than 5.34%, 94.5% less than 10%. Six elite accessions with zero FPR were screened out. The accession-based broad sense heritability of FPR was 0.51. FPR was correlated with domestication and improvement related traits and landraces usually had lower FPR than improved cultivars. Six candidate loci associated with FPR were distributed on five chromosomes. Among them, qFPR-3 on chromosome 18 could be detected by two GWAS analysis methods simultaneously. A candidate gene, Glyma.18G085900, which codes a pentatricopeptide repeat(PPR) superfamily protein and its homologous gene in Arabidopsis is associated with embryo development is determined for qFPR-3 by haplotype analysis. The results of this study not only enable us to deeply understand the situation of FPR in soybean, but also lay a solid foundation for further research on the genetic mechanism of FPR.