Background To summarize the genetic characteristics of GATOR1 complex gene mutations and the surgical prognosis of patients with refractory epilepsy. Methods A retrospective analysis was conducted on 16 patients with GATOR1 complex gene mutations who presented with mainly refractory epilepsy and underwent surgical treatment at the Epilepsy Center of Tsinghua University Yuquan Hospital from May 2019 to August 2024. The follow-up period ranged from 0.5 to 4.0 years. The genetic characteristics, clinical data, treatment, and prognosis of the patients were analyzed. Results Among the 16 patients, 9 were male and 7 were female, with an onset age ranging from 0.6 to 9.4 years, and seizure frequency ranging from once a day to dozens of times a day. Twelve patients (75.0%) had no seizures after surgery, and three of them had completely stopped taking medication. EEG were focal or multifocal, and all clinical seizures were monitored. Two patients had negative MRI. Among the 16 patients, there were 8 with DEPDC5 gene mutations, 5 with NPRL3 gene mutations, and 3 with NPRL2 gene mutations. Conclusions Patients with refractory epilepsy related to GATOR1 complex gene mutations are good surgical candidates, with a high rate of no seizures after surgery. For confirmed patients, surgical treatment should be considered.