In order to explore vegetable and ornamental sweetpotato germplasm resources, we identified more than 1000 accessions in Xuzhou national sweetpotato genebank , and selected 96 outstanding germplasm. 30 pairs of SSR primers were used to analyze genetic diversity and population structure, and genetic differences information of these selected materials was clearly got. 12 phenotypic quality traits data from all the accessions were also analyzed with principal components and clustering analysis. Results were as follows：the total number of amplified bands was 275, in which 269 with polymorphism, and polymorphic rate was 97.8%；Nei72 genetic distance was between 0.15 and 0.76 computed by DPS software with average distance 0.66；Population structure was divided into three groups, which was similar to theclustering results by molecular marker, indicating that those accessions had a greater genetic difference；5 items, 80.4% of active ingredients, were obtained from phenotypic quality traits Principal Components Analysis；96 accessions could be clustered into two groups by phenotypic quality traits markers, and the second group can be divided into three subgroups. Molecular and phenotypic quality traits markers analysis results in this article provided a good reference for the parents selection information for new variety development of vegetable and ornamental sweetpotato.