The invention provides a cigarette chrysanthemum morifolium perfume and a preparation method and application of a micro capsule thereof. The preparation method comprises the steps that dried chrysanthemum morifolium is pulverized, filtering and concentrating are conducted after percolation extraction is conducted to obtain mango extract; the extract is dissolved in ethanol, a ceramic microfiltration membrane and an organic ultrafiltration membrane are utilized to remove large and small molecular impurities respectively, and mango perfume is obtained after pressure reduction and recovery are conducted; water is added to dissolve the mango perfume, an emulsion agent is added to conduct high speed emulsion, a sodium alginate solution is added, uniformly mixed and poured into atomizing condensation equipment to prepare the micro capsule in an atomizing manner, and the micro capsule is received by a calcium chloride solution. The micro capsule is washed by ethanol and pure water, frozen anddried to obtain finished product micro capsule. The invention further provides the application of the micro capsule in cigarettes, the micro capsule is added to a composite filter rod, rolled and produced into a cigarette. After adding the micro capsule, the fragrance amount can be obviously increased, flower fragrance is outstanding, the fragrance is harmony, sweet taste is increased, irritationand impurity gas can be reduced, therefore smoking fume is gentle, and remaining smell is comfortable.