Atmospheric pressure plasma was used to degrade the aflatoxin B1 in acetonitrile. The influence of four independent variables, discharge distance, treatment voltage, discharge time and initial concentration of AFB1, on degradation rate of AFB1 were investigated by single factor test. Based on this, Box-Behnken experiment was designed with degradation rate of AFB1 as response value, the degradation conditions of AFB1 was optimized. The experimental results showed that the factors influencing the degradation rate of AFB1 in acetonitrile were in order as follows: treatment voltage>discharge time>initial concentration of AFB1.The optimum process parameters of degradation of AFB1 by atmospheric plasma were obtained as: treatment voltage of 170V, discharge time of 236 s, initial concentration of AFB1 of 5mg/L, discharge distance of 2cm. Under the conditions, the degradation rate of AFB1 can reach to 92.45%,which is close to predictive value of 93.94% with deviation of 1.49%.