Abstract: The relationship between active ingredient content and antioxidant activity of Cordyceps militaris-Chinese Yam Fungi substance was analyzed. Partial least squares regression was used to establish regression equation of cordycepin,total polyphenols,total flavonoids,total saponins and,total polysaccharides to response of free radical scavenging rate. Then the effect of active ingredient content on antioxidant activity in Cordyceps militaris-Chinese Yam Fungi substance was analyzed. The results showed that,when the number of principal components of the model was two,85% of the total variability could be explained,and the model could fit the experimental data effectively. The influence of cordycepin on free radical scavenging rates were not significant(P>0.05). The total polyphenols had significant positive influence on free radical scavenging rates(P<0.05).The total flavonoids had very significant negative influence on superoxide free radical scavenging rate(P<0.01),but had no significant influence on other free radical scavenging rates(P>0.05). The total saponins had positive influence on free radical scavenging rate,and had very significant influence on hydroxyl free radical scavenging rates(P<0.01). The total polysaccharides had very significant negative influence on free radical scavenging rates(P<0.01). There are mathematical relationship between the active ingredient content and antioxidant activity of cordyceps militaris-Chinese Yam Fungi substance. The effect of the active ingredient on antioxidant activity are not simple superposition,and active ingredients have different effect on antioxidant activity.