<p>Compression pressure and Sodium channel, voltage-gated, type VIII, alpha subunit (<i>SCN8A)</i> and Sodium channel, voltage-gated, type IX, alpha subunit (<i>SCN9A)</i> gene polymorphisms were previously reported to be closely related to postoperative recurrence of trigeminal neuralgia (TN) treated with percutaneous balloon compression (PBC). Patients diagnosed with primary TN who met the criteria for surgery and had a pain intensity score of ≥ III on the Barrow Neurological Institute (BNI) pain intensity scale were included in this study. Patients who had previously undergone PBC treatment and lacked the ability to act independently were excluded. We divided the patients into two groups according to the levels of compression pressure: exposure and non-exposure. Blood samples were also collected for high-throughput sequencing. Based on the follow-up results, the recurrence of PBC-treated TN was assessed and compared between the two patient groups. Furthermore, the association of clinical factors and genetic factors with postoperative recurrence of PBC-treated TN was analyzed. Finally, a prediction model for TN recurrence within 12&#xa0;months post-PBC was constructed. A total of 395 patients were included in this study, with 208 patients in the exposed group and 187 patients in the non-exposed group. There were 251 females (63.54%), with an average age of 66&#xa0;years. Blood samples were provided by 195 patients (102 in the exposed group and 93 in the non-exposed group) for SNP testing. According to the multivariate analysis results, It is also noteworthy that the risk of TN recurrence post-PBC was 0.398 times higher in the exposure group than in the non-exposure group (hazard ratio (<i>HR</i>): 0.398; <i>95% Confidence Interval (CI)</i>: 0.196–0.808; <i>P</i> = 0.011). In TN patients with comorbid hypertension, the risk of recurrence post-PBC was 4.882-fold higher compared to those without hypertension (<i>HR</i>: 4.882; <i>95% CI</i>: 2.023–11.785; <i>P</i> &lt; 0.05). The <i>SCN8A</i> and <i>SCN9A</i> genes have also been associated with recurrence. The results of the codominant model showed that the risk of postoperative recurrence of PBC in patients with rs17125929 heterozygous mutant (TC) was 0.348 times higher than that of patients with rs17125929 wild-type (TT) (<i>HR</i> = 0.348, 95%<i>CI</i> = 0.123–0.988, <i>P</i> = 0.047). The results of the codominant model showed that the risk of postoperative recurrence of PBC in patients with rs36101458 heterozygous mutation (CT) was 0.280 times higher than that of patients with rs36101458 wild-type (CC) (<i>HR</i> = 0.280, 95%<i>CI</i> = 0.110–0.716, <i>P</i> = 0.008). The results of the explicit model showed that the risk of postoperative PBC recurrence in patients with rs36101458-CT TT was 0.396 times higher than that of patients with rs36101458-CC (<i>HR</i> = 0.396, 95%<i>CI</i> = 0.176–0.891, <i>P</i> = 0.025). Allele analysis showed that patients with rs36101458-T had a 0.385-fold higher risk of recurrence after PBC than patients with rs36101458-C (<i>HR</i> = 0.385, 95%<i>CI</i> = 0.192–0.773, <i>P</i> = 0.007). Compression pressure, hypertension, and genetic risk score were further included in the prediction model for the postoperative recurrence of PBC-treated TN. The model's Area Under the Curve (AUC) was 0.813 and <i>Hosmer–Lemeshow χ</i>^<i>2</i> and <i>P</i> values of 2.449 and 0.964. The Decision Curve Analysis (DCA) revealed that the model had the best applicability when the threshold of recurrence post-PBC in TN patients was 0.03–0.55. The results of tenfold cross-validation showed that AUC = 0.782 and Brier Score = 0.131 showed that the model fitted in this study had good repeatability. Our findings revealed that compression pressure and <i>SCN8A and SCN9A</i> gene polymorphisms are crucial factors influencing the recurrence of PBC-treated TN within 12&#xa0;months.</p>