The invention discloses a jujube flavor base, and a preparation method and application thereof. The preparation method for the flavor base comprises the following steps of: 1) performing pre-treatment on jujubes to obtain jujube particles; 2) adding ethanol and performing ultrasonic treatment to obtain jujube extract liquid; 3) performing rotary evaporation and concentration to obtain jujube extract; and 4) performing molecular distillation, separation and purification to obtain a light-component substance, an intermediate-component substance and a heavy-component substance, and performing extraction, overnight standing, filtration and filtrate concentration on the intermediate-component substance to obtain the jujube flavor base. The jujube flavor base of the invention can be used for preparing natural perfume materials for cigarettes and foods, also can be directly used as the natural perfume material, is prepared from the jujubes serving as the raw material, not only has the advantages of transparency, colorlessness, high liquidity and sweet perfume, also has the nutritional and healthcare effects of the jujubes, can be added into the cigarettes to effectively reduce miscellaneous odors in tobacco leaves, improve suction flavor and remaining taste, improve the natural fragrance of the tobacco leaves, comfort throats and treat pharyngitis, and also can be added into the foods to achieve the effects of increasing the flavor and making pure the flavor.