Background: Limited information was known because of the low incidence of co-existence with lung cancer and tuberculosis (TB), it remains special challenging populations for clinical management of cancer immunotherapy. Thus, to investigate the difference on tumour immune microenvironment and genomics between patients with LC alone and LC patients with TB is urgently needed. Methods:Tumour specimens were collected from 87 patients who had LC, with or without TB, at two medical centres. Immunohistochemistry was used to evaluate PD-L1 expression and CD3+/CD4+/CD8+ T-cell infiltration. Whole-exome sequencing was performed using samples from 19 patients with LC&TB and 21 patients with LC. Results:Relative to patients with LC alone, patients with LC&TB had lower PD-L1 expression and CD4+/CD8+ T-cell infiltration (all P< 0.001). A tumour microenvironment with no PD-L1 expression and CD8- T-cell infiltration was most common in the LC&TB patients. Genomic alterations analysis revealed an increased mutation frequency among patients with LC and active TB, obsolete/cured TB, or no TB in terms of the TP53 (23.08% vs. 66.67% vs. 76.19%, P = 0.01), while a decreased trend of the number of single-nucleotide variants/insertions/deletions (P< 0.001), tumour mutation burden (P< 0.001), and number of neoantigens (P< 0.001). Patients with LC&TB had a higher frequency of a specific mutation signature (32.99% vs. 11.23%), as well as potential driver mutations involving the complement C1qB chain (C1QB) mutations. Conclusion: The present study revealed significant differences in the tumour microenvironment and genomic alterations between patients with LC&TB and patients with LC alone.