The invention discloses an HPLC-MS/MS detection method for transgenic maize secondary metabolites, and belongs to the field of liquid chromatography-mass spectrometry detection of maize secondary metabolites. The HPLC-MS/MS detection method for the transgenic maize secondary metabolite comprises the following steps that 1, the secondary metabolites in maize seeds to be detected are extracted, and crude extraction liquid is obtained; 2, the pH of the crude extraction liquid is regulated, the crude extraction liquid is delivered to a solid-phase extraction column to be purified, and eluant is collected; 3, qualitative and quantitative determination is conducted through HPLC-MS/MS. The HPLC-MS/MS detection method which is used for the transgenic maize secondary metabolites and established by optimizing the extraction conditions, the solid-phase extraction conditions, the liquid-phase conditions, the mass spectrometry conditions and the like of the phenolic metabolites in a maize sample is good in sensitivity, has the good reproducibility and stability, has no matrix effect and can be applied to actual detection and analysis of the phenolic metabolites in transgenic maize and non-transgenic maize samples.