Abstract: Using the 3512 optimum regression design with three factors and five levels, effects of applications of Cu, Zn and Se on contents of main active constituents (total flavonoid and chlorogenic acids) and selenium in the flower of Chrysanthemum morifolium were investigated by a pot experiment. The results show that applying Cu, Zn and Se with enough other macro and medium and trace elements is able to increase contents of total flavonoid and chlorogenic acids in the flower of Chrysanthemum morifolium significantly, and the interaction of the three elements also reacts to the influence on the active constituents: contents of total flavonoid and chlorogenic acids are increased significantly under the Cu-Se interaction, however, the contents are decreased under the Cu-Zn and Zn-Se interactions. Higher concentrations of Cu have inhibition or even toxicity effects on the crop growth and the main active constituents. The formation and accumulation of the two main active constituents are restrained under Zn deficiency, and Zn is a dominant nutrient factor of affecting quality of Chrysanthemum morifolium. The effect mechanism of Cu, Zn and Se on the active constituents should be further studied. There is significant positive correlation between selenium content of the flowers and Se application amount. The selenium content of the flowers is not able to be influenced by the application of Cu and Zn. This result provides theoretical basis for developing Se enriched Chrysanthemum morifolium Ramat and its series products.