Abstract Cyclocarya paliurus is a highly valued and multiple function tree species. Its leaves have traditionally been used as a medicine or nutraceutical tea. However, limited information is available on its genotype selection and cultivation under a wide range of environmental conditions for growth and enhanced antioxidant activities. Twelve genotypes of C. paliurus at four sites were assessed with respect to genotype, environment and their interaction on growth and flavonoid accumulation, while adaptability and stability of each genotype to varying growth environments were also examined. Results indicated that genotype and growth environment significantly affected the growth and flavonoid accumulation of C. paliurus, with environmental effects being more predominant. Interactions between genotype and environment significantly influenced flavonoid accumulation, but not in growth. Across four sites, stability in tree height growth and total flavonoid content of leaves varied among 12 genotypes of C. paliurus. Hierarchical cluster analysis based on height growth and total flavonoid content of leaves indicated the 12 genotypes were classified into four distinct groups, and three genotypes (SC-4, HF-10 and KM-5) were recommended for flavonoid production in future. Techniques used in this paper would be valuable in identifying the best choice among current and future genotype of C. paliurus for use in flavonoid production.