The cyanogenic glycoside in flaxseed has certain toxicity and its existence limits the comprehensive utilization of flaxseed. In this study, plasma technology was used to treat flaxseeds, and the effect of treatment dose intensity, seed flow rate per unit time and treatment times on the cyanogenic glycoside of flax were studied. The result of orthogonal test showed that the order of factors influencing the content of cyanogenic glycoside in flaxseed was dose intensity＞treatment times＞seed flow. The optimal combination of plasma seed treatment was: the dose intensity is 2.4 A, the treatment times are 4, and the seed flow rate is 0.8 kg/min. The results showed that the content of cyanogenic glycoside in different flax varieties treated by plasma technology decreased in varying degrees, with a decrease range of 18.14%-31.33%. The research shows that the plasma technology can effectively reduce the content of cyanogenic glycosides in flaxseed and can be applied in production practice.