Background: Intratumoral heterogeneity (ITH) is associated with the poor prognosis in a variety of solid tumors. However, the use of ITH as a predictive biomarker for immunotherapy in patients with advanced non-small cell lung cancer (NSCLC) is still lacking. Methods: We used the Bioconductor R package Maftools to analyze somatic variants of NSCLC from an independent cohort (Hellmman CM012 study cohort) with data from 75 patients with advanced NSCLC. We then used a mutant-allele tumor heterogeneity (MATH) algorithm to measure ITH and analyzed the correlation with immunogenic marker, and the prognostic effect of ITH on immunotherapy. Results: The objective response rate (ORR) and durable clinical benefit (DCB) of immunotherapy was 36.5% and 53.8% for the patients with low ITH (ITH-L), and 21.7% and 39.1% for the high ITH (ITH-H) subgroup (P = 0.0427, P = 0.3180). The ITH-L patients had significantly improved median progression free survival (mPFS) than the ITH-H group (7.98 versus 2.60 months, hazard ratio (HR) = 1.88, 95%CI 1.06−3.34, P = 0.0280). The ORR and DCB of immunotherapy was 45.9% and 59.5% for the patients with high TMB (TMB-H), and 18.4% and 39.5% for the low TMB (TMB-L) subgroup (P = 0.0354, P = 0.1077). The TMB-H patients had significantly better mPFS than the TMB-L group (8.12 versus 3.78 months, HR = 0.49, 95%CI 0.28−0.87, P = 0.0130). A pooled analysis of ITH and TMB show that mPFS and ORR in the TMB-H+ITH-L group was significantly better than that in the TMB-H+ITH-H, TMB-L+ITH-H, TMB-L+ITH-L group (P = 0.0099, P = 0.0121). A subgroup analysis of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) found that ITH-L was associated with better mPFS (ITH-L versus ITH-H = 8.71 versus 2.17, HR = 3.42, 95%CI 0.96−12.23, P = 0.0460) in LUSC, and no significantly mPFS benefit was found in the ITH-L group in LUAD (ITH-L versus ITH-H = 7.98 versus 5.09, HR = 1.69, 95%CI 0.88−3.26, P = 0.1100). There was no significant difference in TMB levels between ITH-L and ITH-H groups (13.8 Muts/Mb versus 14.2 Muts/Mb, P = 0.2139). Conclusions: ITH may serve as a positive predictor of immunotherapy in patients with advanced NSCLC, especially in LUSC and their clinical value warrants further investigation.