The invention discloses a construction method and identification application of fingerprint spectra of natural apis cerana honey of lychee flowers and natural apis mellifera honey of lychee flowers. GC/MS fingerprint spectra of the natural apis cerana honey of lychee flowers and natural apis mellifera honey of lychee flowers are separately constructed by a headspace solid-phase microextraction-gaschromatography-mass spectrometry method and a traditional Chinese medicine fingerprint similarity evaluation system; and it determines that the GC/MS fingerprint spectrum of the natural apis cerana honey of lychee flowers contains 19 common feature volatile components, and the GC/MS fingerprint spectrum of the natural apis mellifera honey of lychee flowers contains 16 common feature volatile components. By comparison of similarity and chemical composition difference of a total ion chromatogram of a to-be-detected natural honey sample of lychee flowers and a constructed GC/MC fingerprint spectrum, the natural apis cerana honey of lychee flowers and the natural apis mellifera honey of lychee flowers are accurately distinguished and identified. The method has the characteristics of small useamount of the sample, high characteristics and reliable result, the problem that the natural apis cerana honey of lychee flowers and the natural apis mellifera honey of lychee flowers in markets aredifficult to distinguish is solved quite beneficially, and the social benefit is quite obvious.