While the intratumoral microbiota has been discovered to have a close connection with tumor immunity, the specific role played by intratumoral microbiota in regulating the tumor immune microenvironment (TIME) of lung cancer remains largely unexplored. Here, we comprehensively investigated the association between intratumoral microbiota and the TIME in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). First, we found that intratumoral microbiota and host transcriptome profile significantly differed between LUAD and LUSC. Moreover, there were strong associations between abundance of intratumoral microbes and expression of host genes in both LUAD and LUSC. Furthermore, we found an association between intratumoral