Percutaneous balloon compression (PBC) offers substantial immediate relief from the severe pain associated with trigeminal neuralgia (TN). To investigate the effect of compression Frequency during balloon compression on facial numbness in patients with primary trigeminal neuralgia, we conducted a nested case–control study. A retrospective analysis was performed on clinical data from 150 TN patients treated with PBC from October 2017 to May 2022. Of these, 60 patients underwent a single PBC compression, while the remaining 90 underwent two compressions. The Barrow Neurological Institute Pain Intensity (BNI-P) score was employed to measure the severity of pain. The Barrow Neurological Institute facial numbness score (BNI-N) was used to assess the degree of postoperative pain relief and facial numbness. At time point T1, the BNI-P scores for the “two compressions” group were significantly lower than those for the “single compression” group (P < 0.05). From T2 to T5, no significant differences in BNI-P scores were observed between the groups. For the BNI-N score, there was no notable difference between the groups at T0, while from T1 to T4, the “double compressions” group exhibited significantly lower BNI-N scores than the “single compression” group (P < 0.05). At T5, no significant difference in BNI-N scores was observed between the groups. The application of two compressions in PBC is a safe and effective surgical method that not only maintains the efficacy of the procedure but also significantly reduces the degree and duration of postoperative facial numbness.