The invention relates to a method for identifying the variety of honey by use of a non-target metabonomics technology. The method is characterized in that through a simple sample pre-treatment process, then lots of high-resolution mass spectrometric data are acquired through an ultra-high performance liquid chromatography-quadrupole/electrostatic field orbitrap high-resolution mass spectrometry method, interference caused by deviation and variation in experimental data through background deduction, chromatographic peak extraction, normalization, data conversion and data scaling, and after that, a real feature marker capable of distinguishing the variety of honey can be discovered and confirmed through principal component analysis, t-checkout, volcano plots and variable importance projection drawings. When the feature marker is utilized to identify the quality of honey, the identification results are objective and accurate. The method is used for not only source-tracing identification of the variety of honey but also variety source tracing and origin tracing identification of other agricultural products.