Background: Previous studies have shown that intra-tumor heterogeneity (ITH) can lead to drug resistance to tumor therapy, which is associated with poor prognosis of solid tumors. However, studies on the correlation between ITH and immunotherapy efficacy in patients with advanced bladder cancer (BLCA) are still lacking. Methods: Bioconductor R package Maftools was used to analyze somatic variants of advanced BLCA from an independent cohort (Miao-249 study cohort, PMID: 30150660) with data from 27 patients who underwent whole-exome sequencing. The ITH score was measured using the mutant-allele tumor heterogeneity (MATH) algorithm to analyze the difference in the genetic profile between the ITH score high (ITH-H) and ITH score low (ITH-L) groups, its association with tumor mutational burden (TMB), and the effect of ITH on the prognosis of immunotherapy. Results: There were significant differences in gene mutation spectrum between ITH-H and ITH-L groups. The genes with the highest mutation frequency in ITH-H group were TP53 (57.14%), DNAH5 (38.1%), TNRC18 (38.1%), TTN (38.1%), CSMD3 (33.33%), MDN1 (33.33%), MRPL49 (33.33%), and MUC19 (33.33%), while the genes with the highest mutation frequency in ITH-L group were KDM6A (83.33%), TP53 (66.67%), CALN1 (50%), MICAL2 (50%), MTOR (50%), NINL (50%), PCDHA (50%), and RMIBP2 (50%). The objective response rate (ORR) of immunotherapy was 66.66% and 42.86% for the patients with ITH-L and ITH-H subgroup. The ITH-L patients had significantly improved median overall survival (mOS) than the ITH-H group (not reach versus 12.3 months, hazard ratio (HR) = 6.65, 95%CI 0.86−51.36, P = 0.037). There was no significant difference in median TMB levels between ITH-L and ITH-H groups (8 Muts/Mb versus 7.6 Muts/Mb, P = 0.97). The TMB high (TMB-H) patients had no significantly better mOS than the TMB low (TMB-L) group (not reach versus 9.07 months, HR = 0.33, 95%CI 0.07−1.49, P = 0.13). A pooled analysis of ITH and TMB show that mOS in the ITH-L+ TMB-H group was numerically better than that in the ITH-H+TMB-H, ITH-H+TMB-L, and ITH-L+TMB-L group (not reach versus 15.6 months versus 7.1 months versus not reach, HR-1.57, 95CI 0−Inf, P = 0.1). Conclusions: The results suggest that ITH may be independent of TMB and a positive predictor of immunotherapy in patients with advanced BLCA.