Chromatography is widely used in components separation and detection. Since mycotoxins display toxicity even at low concentration, they can be separated and detected in trace by chromatography. Different chromatography methods were applied according to the characteristics of the mycotoxins. Thin layer chromatography (TLC) is suitable for rapid qualitative of mycotoxins. Gas chromatography (GC) prefers to detect the mycotoxins after derivatization and vaporization. Liquid chromatography (LC) is only applied to analyze the mycotoxins with or without derivatization which were of ultraviolet and fluorescence absorption, while for those without ultraviolet and fluorescence absorption use mass spectrometry detector. The features of the qualitative and quantitative analysis on mycotoxins were introduced, which provides a theoretical basis for the subsequent use of chromatographic method in application of detection on mycotoxins, especially synchronous detection of multiple mycotoxins in samples.