A microwave irradiation technique was applied for degradation of aflatoxin B1(AFB1) in corn flour, and immunoaffinity column clean-high performance liquid chromatography-post-column derivatization method was applied to determine the content of AFB1. The effects of microwave power, irradiation time and initial quality of AFB1 on degradation efficiency were investigated. Microwave irradiation was compared with conventional heating method. The results showed that the degradation of AFB1 was performed by non-thermal effect. The optimized microwave power was 250 W and irradiation time was 30 min. Under this condition, the degradation rate would reach to 90%. The residues of AFB1 were in the safety limit range of the national standard and the European Union. The nutrition quality of corn flour was slightly affected by the microwave irradiation treatment. The toxicity of AFB1 was reduced obviously and there was no secondary pollution. Therefore, the microwave irradiation can be used as an effective method for the degradation of AFB1. 