Assessing the authenticity about the botanical and geographical origins of food is an important content for food safety research. Amino acids are the most important nutrients of honey. The types and contents of amino acids are different in various honey samples. Thus they can be used as one of the important parameters to discriminate the honey variety and quality. In this article, amino acids in honey were first derived with formaldehyde and acetyl acetone solution. In the following step, three-dimensional fluorescence spectrums combing with multidimensional pattern recognition methods were used to distinguish the kinds of honey. Five kinds of honey (total 150 honey samples) from different botanicals were studied in this research. Before fluorescence detection, the effect of the amount of derivation reagent, the time of reaction, temperature and pH to the derivation progress of honey samples were first studied. Research showed that the fluorescence intensity of derivatives of honey was the strongest when the amount of derivation reagent was 4.0 mL, the time of reaction being 2 h, pH being 4 and the temperature being 100 ℃. The derivatives of honey were then scanned with three-dimensional fluorescence spectrometry. The collection of fluorescence intensity values occurred within excitation-emission ranges of 300~500 and 380~580 nm. A 150×41×101 cube matrix data sets can be acquired. The three-dimensional fluorescence data sets were decomposed with multilinear pattern recognition methods, such as multilinear principal components analysis (M-PCA), self-weight alternative trilinear decomposition (SWATLD) and multilinear partial least squares discriminant analysis (N-PLS-DA) methods. All of these multilinear pattern recognition methods showed the clustering tendency for five different kinds of honey. Compared with the other two methods, N-PLS-DA got more accurate and reliable classification results because it made full use of all the fluorescence information of the derivative honey samples. Its total recognition rate reached 88%. The result is acceptable for the complexity of the honey samples. It showed this method could be applied to identify the varieties of honey. Compared with the chromatographic analysis method, this method is relatively simpler and more sensitivity. It avoided the chromatographic separation and reduced the consumption of organic solvent. Thus it can be regarded as a kind of relatively green honey classification method. This research will provide a new idea to directly fluorescence analyze for no or weak fluorescence natural substances.