With the decrease in the number of natural populations of Actinidia arguta, there is an urgent need to collect A. arguta germplasm resources and explore their genetic diversity for better management and protection. In this study, 31 simple sequence repeat (SSR) markers were used to identify 148 wild A. arguta germplasms from six natural populations in Changbai Mountain, China, and the genetic diversity of their leaf quality traits was subsequently evaluated. SSR analysis revealed rich genetic diversity among different individuals and within populations of A. arguta. Molecular variance analysis determined that the genetic diversity of wild A. arguta mainly came from within the populations (95% variance component ratio), while only a small part originated from among populations (5% variance component ratio). Abundant genetic variations were observed in the leaf quality traits of the different A. arguta resources with a high genetic diversity index (0.13–1.23). Leaf quality trait clustering and the unweighted pair group method with arithmetic average (UPGMA) clustering analysis showed similar classification results. Population structure analysis divided 148 individuals into three subgroups. Our results indicate that the populations of A. arguta in Changbai Mountain have large genetic variation and high genetic diversity. This study broadens the genetic basis of the A. arguta breeding germplasm.