Job’s tears (Coix lacryma-jobi L.) is a superior crop used as food and herbal medicine. For the better utilization and conservation of Chinese Job’s tears germplasm, principal component analysis and cluster analysis were used to analyze the 15 seed morphological characteristics of 36 Job’s tears accessions. The results indicated that the 36 Job’s tears accessions possess high morphological characteristics diversity. Variations were recorded for the 4 qualitative seed morphological characteristics measured. One-way ANOVA showed very significant differences between accessions for the 11 quantitative seed morphological characteristics. Coefficient of variation ranged from 8.43% to 68.01% with the maximum value recorded in weight of the hull and the testa and the minimum value recorded in seed length. Principal component analysis divided the 36 Job’s tears accessions into 3 groups, which corresponded to the central and south, north, and wild groups, respectively. The morphological characteristics of the 3 groups were significantly different. Cluster analysis divided the 36 Job’s tears accessions into 5 groups, including the central and south group, the north group and 3 wild groups. Six Job’s tears accessions FJNJ, TJ-BK-1, TJ-BK-2, MY-BK-1, MY-BK-2 and JYSD were preliminary selected as accessions with high anticancer activity.