Cyclocarya paliurus is a sole medicinal tree species in China. However, limited information is available on its genotype selection for improving growth and flavonoid production. In this study, we analyzed the growth and flavonoid accumulation in 33 families of Cyclocarya paliurus from 12 provenances. Results indicated that tree height and diameter at breast height growth were significantly influenced by provenance and family, while provenance had more important impact. The contents of total and individual flavonoids (quercetin, isoquercitrin, and kaempferol) were significantly influenced only by family, which accounted for 86% of total variation. The growth and flavonoid accumulation of C. paliurus showed a distinct geographic variation pattern. The hierarchical cluster analysis based on the growth and flavonoid contents in leaves indicated that 33 families of C. paliurus can be classified into 4 distinct groups.