Bladder cancer is one of the most common malignant tumors in urology in China. The analysis of gene mutation in bladder cancer and its relationship with clinical characteristics and prognosis will provide a basis for accurate treatment of bladder cancer. The aim of this study was to analyze the mutations and functional regions of bladder cancer-related genes based on high-throughput sequencing, and to explore the relationship between mutations and clinicopathological features, as well as its prognosis and clinical implication. From April 2020 to October 2020, a total of 47 patients with bladder cancer in the Department of Urology, Affiliated Hospital of Chengde Medical College were studied. Gene sequencing was performed using Nextseq CN500 System, a high-throughput sequencing platform. The results of gene detection were described, and the relationship and clinical value of high frequency mutated genes with clinicopathological features and prognosis were systematically analyzed. A total of 29 mutation genes, 61 exons, and 95 mutation sites were identified in this study. The frequencies of TP53, FGFR3, PIK3CA, ERBB2, MUC4, and KRAS mutation are relatively high, accounting for 59.92 % of the total mutation frequency. The TP53 was significantly associated with muscle invasive bladder cancer, T2 stage, and progression-free survival, while FGFR3 was significantly associated with non-muscle invasive bladder cancer and T1 stage. High-throughput sequencing technology provides a successful approach for detecting bladder cancer gene mutations. The TP53, FGFR3, PIK3CA, ERBB2, MUC4, and KRAS genes have high mutation frequencies in bladder cancer patients. The TP53, FGFR3 and PIK3CA genes may play a predictive role in the prognosis of bladder cancer, which may hold certain guiding significance for in-depth study of the pathogenesis of bladder cancer and the development of targeted therapies.