Cyclocarya paliurus is widely distributed in subtropical areas of China. Secondary metabolites in the leaves, including flavonoids and triterpenoids, provide protection against diseases such as hyperlipidemia, diabetes, hypertension, and hypoimmunity. In this study, 343 C. paliurus leaves were collected from 32 distinct populations covering most of the main distribution, to deduce the response of flavonoids and triterpenoids to seven environmental factors. Principal component analysis was performed using seven flavonoid and six triterpenoid compounds. The results show that altitude, latitude, and longitude significantly contributed to variations in total flavonoid and triterpenoid contents. In addition, the interaction of these metabolites was extensively correlated with environment changes, and therefore should be considered during selection and cultivation.