The invention discloses a natural apple essence and a preparation method thereof. The natural apple essence is prepared by carrying out blending modification on apple concentrate. The preparation method of the natural apple essence comprises the following steps of: (1) carrying out inspection, washing and crushing on raw material apples, then juicing, filtering juice to obtain supernatant, and concentrating the supernatant to the relative density of 1.050 to 1.250 by a vacuum concentration device to obtain the apple concentrate; and (2) carrying out blending modification on the apple concentrate. Not only does the preparation method of the natural apple essence, which is disclosed by the invention, overcome the defect of large using amount of a compound in a cigarette essence in the prior art, but also the natural apple essence prepared by the method has stronger natural taste, is purer, has excellent effect, can be coordinated with the fragrant of cigarettes, improves the smoking quality of the cigarettes and has an obvious effect of improving the smoking quality of the cigarettes.