This study presents the bioactive compounds, antioxidant, antibacteria, and anti-inflammation of C. militaris fruiting body (FB) and FB with substrate (FBS). C. militaris FB and FBS were extracted by water, ethanol, and methanol. The chemical composition analysis of C. militaris extracts from FB and FBS showed bioactive compounds including adenosine, cordycepin, and carotenoids using HPLC. Moreover, the aqueous extract of FB and FBS showed the highest antioxidant activity against DPPH and ABTS radicals, supported by the presence of adenosine, cordycepin, and carotenoid compounds. Moreover, the ethanolic and methanolic extracts of C. militaris and the bioactive compounds, cordycepin and carotenoids, exhibited the greatest bactericidal activity against enteric pathogenic bacteria. In addition, C. militaris extracts and bioactive compounds were confirmed as new agents to prevent the adhesion and invasion of enteric pathogenic bacteria on Caco-2 colon cells. This finding also demonstrated the anti-inflammatory activity found in the aqueous extract of C. militaris and bioactive compounds on the LPS-stimulated Caco-2 cell model, which had the efficacy to suppress inflammatory moderators including iNos, Cox-2, NF-kappa B, TNF-alpha, AP-1, TLR-4, IL-1 ss, and IL-6. Therefore, C. militaris extract and its bioactive compounds, cordycepin and carotenoids, impeded the adhesion and invasion of enteric pathogenic bacteria on colonic epithelial cells and also promoted anti-inflammation mechanisms. This study attests to C. militaris as an alternative therapeutic agent to prevent enteric pathogenic bacterial infection and inflammation due to its proven health benefits and high level of antioxidants.