The invention discloses a Lonicera japonica fermented extract and a preparation method and application thereof. The Lonicera japonica fermented extract is prepared from Lonicera japonica, which serves as a raw material, through fermenting with Lodderomyces elongisporus and extracting aroma components from a fermented solution. The Lodderomyces elongisporus is collected in the China General Microbiological Culture Collection Center (CGMCC); the collection number is CGMCC No. 6645; the collection date is October 08, 2012. The product contains a variety of aroma substances, such as phenylethyl alcohol, palmitic acid, ethyl palmitate, linoleic acid, methyl 9,12,15-octadecatrienoate, myristic acid (tetradecanoic acid), pentacosane, lauric acid, linalool, leaf alcohol and the like. Shown by results of flavored smoking assessment tests, the product can be harmonized with cigarette flavors, can obviously promote the cigarette flavors, make smoke gas delicate and mellow, lower irritation, conceal impurity gases and improve the smoking flavor of cigarettes, and can generate a fresh and special aroma.