Abstract: Cornus officinalis is widely distributed in the provinces along the Yangtze River of China. Due to the effects of soil and climatic factors, there exists a greater variation in the morphology of C. officinalis seeds in different regions. In this study, the seeds of seven C. officinalis natural populations were collected from four provinces  to study the phenotype variation in the seed morphology (seed length, seed width, seed volume, and coefficient of seed shape) and its correlations with environmental factors, the geographical variation trend of the seed morphology, and the clustering of the populations. There existed significant differences in the seed morphology among the seven populations. The seed width had a significant positive correlation with the seed volume, and the two variables had significant negative correlations with latitude, presenting an obvious geographic variation trend. Based on the cluster analysis of the seed morphological traits, the seven populations could be classified into two groups, i.e., northern group, including the populations in Fuping and Hanzhong of Shaanxi and in Lunchun of Henan, and southern group, including the populations in Ningguo, Huangshan, and Jingde of Anhui and in Zhenjiang of Jiangsu. This study could provide references for the screening of suitable C. officinalis provenances in different cultivation regions.