Pilonidal sinus disease (PNSD) challenged surgeons for decades. Limberg flap repair (LFR) is a common treatment for PNSD. The purpose of this study was to observe the effect and risk factors of LFR in PNSD. A retrospective study was conducted on the PNSD patients who visited two medical centers and four departments in the People's Liberation Army General Hospital and were taking LFR treatment between 2016 and 2022. The risk factors, the effect of the operation, and complications were observed. The effects of known risk factors on the surgical results were compared. There were 37 PNSD patients: male/female ratio of 35:2, average age: 25.1 ± 7.9 years. Average BMI: 25.2 ± 4.0 kg/m2, average wound healing time: 15.4 ± 3.4 days. 30 patients (81.0%) healed in stage one and 7 (16.3%) had postoperative complications. Only 1 patient (2.7%) had a recurrence while others were healed after dressing‐changing. There was no significant difference in age, BMI, preoperative debridement history, preoperative sinus classification, Wound area, Negative pressure drainage tube, prone time (<3d) and treatment effect. Squat defecate and premature defecation were associated with treatment effect, and they were independent predictors of treatment effect in the multivariate analysis. LFR has a stable therapeutic outcome. Compared with other skin flaps, the therapeutic effect of this flap is not significantly different, but the design is simple and is not affected by the known risk factors before operation. However, it is necessary to avoid the influence of two independent risk factors, squatting defecation and premature defecation, on the therapeutic effect.