The morphological genetic diversity and population phenotypic characteristics were evaluated by principal component analysis and cluster analysis among 103 soybean landraces collected from Chongqing. The results showed that gray pubescence, yellow seed coat and brown hilum were detected in the majority of the tested soybean accessions, and larger variation in quantitative traits were shown among individual accession. Three main principal components reflected most information over 10 agronomic traits, and the main agronomic traits of soybean landraces could be summarized as yield factors, growth potential factors and grain factors. Cluster analysis divided the 103 soybean landrace into 6 subgroups. Although a few accessions showed distinct differentiation, germplasms collected from the same district showed widely similarity in morphological characteristics. Genotypic differentiation among soybean subgroups had a certain but not absolute correlation with geographic distribution. In addition to utilizing geographical-distant germplasms, exploiting the potentialities of genetic variation of characters within the landraces should be considered in selection of parents of breeding.