The aims of this research were to production of high bioactive compounds in fruiting bodies of Cordyceps militaris cultivation and its applications for disease protection and/or therapy in commercial used. The appropriate factors for high bioactive compound production using media supplemented with pupae and porcine liver dried powder by ratio of 1:1 as 10 g/L adding in basal media, and the blue LED light induction of mycelia growth and white LED light induction during fruiting body formation, resulting in higher significant (p < 0.05) yields of cordycepin and adenosine as 713.33 and 41.58 mg/100 g, respectively which compared to the other groups. The crude water extract of this C. militaris having cordycepin and adenosine as 834.6 and 308.86 mg/100 g, respectively. The comparison of crude polysaccharide extracts showed that the yields of the 4 crude extracts samples were not significantly different (p > 0.05), which were in the range of 41.02 - 41.79%. The antioxidant properties including DPPH radical scavenging assay, improved ABTS radical cation decolorization assay, superoxide radical scavenging assay, hydroxyl radical scavenging assay, ferrous chelating and ferric reducing power were found to be different (p < 0.05). It was found that the C. militaris crude polysaccharide extracts from defatted and ultrasonicated preparation had the better antioxidant properties compared with those without defatted and sonicated. The C. militaris crude water extract had an IC50 value of 63 mgAAE/g extract, and the growth inhibition of liver and colon cancer cells as IC50 values of 2.329 and 0.873 mg/ml, respectively. The activities of this C. militaris crude water extract were also investigated in rats. The experimental groups were divided into 6 groups: group 1, normal rats, groups 2 - 6 received CCl4 to induce liver injury, with group 2 force fed with distilled water, groups 3 - 5 force fed for 30 days with 12.5, 25 and 50 mg/head/day, respectively, and group 6 force fed with 100 mg/ kg Salymarin. The results showed that feeding the crude extract at 25 mg/kg body weight resulted in the levels of AST, ALT and ALP enzymes similar to those in the control group. The histological evidences of the liver indicate that helping the damaged liver cells return to function similar to normal mice, resulting in the levels of BUN and creatinine were not differenced from normal mice. And all this extract groups will increase the rat’s hematological value equal to normal rats at all measured values. The amount of this extracts were not affected by the changes in the white blood cell types in rats.These results indicated that the C. militaris with high bioactive compounds might be as medicinal efficacy as good antioxidant, anticancer, and in rat liver damage protection and immune stimulation.