According to two-factor quadratic regression rotation design, effects of water and nitrogen fertilizer coupling on yield and quality of Chuzhou Chrysanthemum morifolium were studied by a pot experiment and the suitable water and nitrogen management modes were investigated. Results showed that remarkable effects of water and nitrogen coupling on flower yield, total flavonoid content of leaf or flower, chlorogenic acid content of leaf or flower of Chuzhou Chrysanthemum morifolium were displayed, and there was a significant interaction between water and nitrogen. Effects of water on flower yield, total flavonoid content and chlorogenic acid content were more significant than those of nitrogen fertilizer. When soil water and nitrogen fertilizer were at 0.2841 and 0.4037 levels, respectively, namely, keeping 80% of the field water capacity and 0.257 g/kg nitrogen fertilizer, flower yield of Chuzhou Chrysanthemum morifolium reached a maximum up to 18.09 g/plant; and when both of soil water and nitrogen fertilizer were at -1.414 level, namely, keeping 50% of field water capacity and 0 g/kg nitrogen fertilizer, total flavonoid content and chlorogenic acid content of Chuzhou Chrysanthemum morifolium flower were maximal. Considered from the field of flower yield and quality, a suitable management mode of water and nitrogen is to keep middle level in the beginning stages of growth of Chuzhou Chrysanthemum morifolium and low level in the squaring stage and flowering period.