The invention discloses a method for detecting fungal pollution producing aflatoxin by combining GC-IMS and fluorescence spectrum, which comprises the following steps: performing sample treatment, GC-IMS detection, fluorescence spectrum detection, GC-IMS spectrogram characteristic region selection, fluorescence spectrum characteristic region selection, data characteristic extraction and fusion of GC-IMS and fluorescence spectrum detection, principal component analysis on the extracted feature data, then extractiion of principal components of first ten dimensions of PCA of the two data sources as novel feature vectors, and direct combination of the novel feature vectors together to form fusion data; and performing orthogonal partial least squares discrimination on the fused data, inputting the data after feature fusion into an orthogonal partial least squares discrimination model, taking a test set sample data feature value of a fused signal as input, and obtaining a final classification model through an orthogonal partial least squares discrimination algorithm, so that the method is applied to detection of an unknown sample. The method is simple and easy to operate, operation cost is reduced, and the method has good classification performance and high popularization and utilization value.