The invention relates to an application system of chemical apparatus analysis, and especially relates to an ion chromatography-carbon nanotube-modified electrode electrochemical detection analysis system used for simultaneously detecting folic acid and methotrexate. The invention relates to an ion chromatography-carbon nanotube-modified electrode electrochemical detection analysis system. According to the invention, the carbon nanotubes are positively charged through covalent modification, and are absorbed on the surface of bare glass carbon electrode, such that novel carbon nanotube membrane-modified electrode is formed. The modified electrode is adopted as a working electrode, such that methotrexate and folic acid in anion states can be easily absorbed. Compared to bare glass carbon electrode, electrocatalytic oxidation of methotrexate and folic acid are greatly promoted. According to the invention, the modified electrode is applied in combination with ion chromatography in an ion chromatography electrochemical detector, such that methotrexate and folic acid rapid separation and detection are realized. Therefore, a problem that separation cannot be realized by using merely electroanalysis, and defects of low sensitivity, high interference and complicated operation of other detection methods, are overcome. The system is suitable for detections of low-concentration methotrexate and folic acid in complex substrate biological samples.