Abstract: Pot experiments were carried to study effects of ecology and varieties and their interaction on polyphenols contents in flue-cured tobacco in Henan, Yunnan and Guizhou. NC89, K326 and Honghua Dajinyuan were planted on each location, where other planting conditions maintaining as consistently as possible. The results showed that ecology and varieties and their interaction had significant effects on total polyphones, rutin, and chlorogenic acid in flue-cured tobacco leaves. Among them, the contributing ratios of ecology to the content variation of total polyphones, rutin, and chlorogenic acid were 24%, 55% and 47%, respectively. The variety were 2%, 36%, 18% and their interaction were 74%, 8% and 35%. The interaction results of ecology and variety indicated that the total polyphenols and chlorogenic acid content were higher under the interaction condition of NC89 and Henan ecology, the chlorogenic acid content was higher under the interaction of K326 and Henan ecology; the total polyphenols and rutin content were higher under the interaction of K326 and Yunnan ecology, The total polyphenols, rutin and chlorogenic acid content were higher under the interaction of Honghuadajinyuan and Guizhou ecology. In conclusion, the ecology and the interaction of ecology and variety were the key factors which affected phenols compounds content in flue-cured tobacco.