Background <p>The tumor downstaging and pathological complete response of bladder cancer were found to be improved with the application of neoadjuvant chemotherapy combined with immunotherapy. However, about 34.2% of patients with muscle-invasive bladder cancer were insensitive or unresponsive to neoadjuvant chemoimmunotherapy. Despite the diversity of biomarkers for therapeutic effect of neoadjuvant immunotherapy or chemotherapy, biomarkers to accurately evaluate the therapeutic effect and toxicity of neoadjuvant chemoimmunotherapy in bladder cancer are currently lacking. To identify potential genomic biomarkers for the responsiveness of neoadjuvant chemoimmunotherapy, we analyzed the genomic dynamic changes of patients with muscle-invasive bladder cancer.</p> Results <p>Five patients were sensitive to neoadjuvant chemoimmunotherapy and were in the response group, while the other 5 patients were insensitive to neoadjuvant chemoimmunotherapy and were in the resistance group. Before neoadjuvant chemoimmunotherapy, the number of sequenced genes was higher in the response group than in the resistance group (<i>P</i> = 0.002), and this difference persisted at the end of chemoimmunotherapy (<i>P</i> = 0.014). After neoadjuvant chemoimmunotherapy, 256 mRNAs were up-regulated and 394 mRNAs were down-regulated in the resistance group, while 773 mRNAs were up-regulated and 296 mRNAs were down-regulated in the response group. In addition, there were significant differences in mRNA expression between the response group and the resistance group before and after neoadjuvant chemoimmunotherapy. By comprehensively considering the dynamic changes of mRNA expression before and after neoadjuvant chemoimmunotherapy in the response group and the resistance group, 7 genes, including PTHLH and S100A2, which may be related to the resistance of chemoimmunotherapy in bladder cancer were finally screened. The results of GO and KEGG enrichment analysis showed that upregulated mRNAs in the resistance group were mainly related to sialyltransferase activity, regulation of ROS metabolic process and HIF-1 signaling pathway, while downregulated mRNAs were mainly involved in the regulation of NADH dehydrogenase activity and oxidative phosphorylation.</p> Conclusion <p>Our study is the first to identify molecules and pathways closely related to treatment resistance based on dynamic transcriptome changes before and after neoadjuvant chemoimmunotherapy in bladder cancer, and to find that genes such as PTHLH and S100A2 may be involved in the resistance of chemoimmunotherapy in bladder cancer.</p>