Schisandra chinensis (Turcz.) Baill. has been traditionally used as a medicine for bronchial tube ailments in Northeast Asia. Recently, the demand for S. chinensis has increased for use as food and medicine because of the lignans found in its fruits. However, the species germplasm collection has rarely been studied to evaluate their phenotypic traits in Korea. In this study, 96 accessions of S. chinensis were collected in South Korea for two years to evaluate their phenotypes, and principal component analysis (PCA) and cluster analysis were conducted. Significant variations among the measured phenotypic traits were observed. The total bunch weight produced from a single tree ranged from 109 to 5844 g; the contents in schizandrin, gomisin A, and gomisin N—three types of lignan—were 2.2–14.5, 0.9–9.8, and 2.1–12.2 mg/g, respectively. Gomisin N positively correlated with flowering traits (flowering start, period, and peduncle length) and leaf characteristics (leaf width and length). PCA and cluster analyses revealed four clusters among the 96 S. chinensis accessions. These results provide valuable information for systematic characterization of species germplasm collections and tools for further research.