Objective To investigate short-term clinical outcomes of double-modified Limberg flap transplantation in treatment of sacrococcygeal pilonidal sinus. Methods One hundred patients with sacrococcygeal pilonidal sinus from October 2010 to May 2015 in this hospital were included, and subsequently were divided into double-modified Limberg flap transplantation group (double-modified flap group,n=30), classical Limberg flap transplantation (classical flap group,n=30), and interrupted suture after resection group (interrupted suture group,n=40). The duration of operation, intraoperative bleeding, hospital stay, duration of return to work, recurrence rate, and incision complications rate were compared among these three groups. Results ① The age, gender, body mass index, and preoperative complications had no significant differences among these three groups (P>0.05). ② The intraoperative bleeding and the hospital stay had no significant differences among these three groups (P>0.05). Compared with the interrupted suture group, the durations of operation were significantly longer (P<0.05), the durations of return to work were significantly shorter (P<0.05), the recurrence rates were significantly lower (P<0.05) in the double-modified flap group and the classical flap group. The above indicators had no significant differences between the double-modified flap group and the classical flap group (P>0.05). ③ The incision hematoma and the part disruption of incision had no significant differences among these three groups (P>0.05). Compared with the interrupted suture group, the rates of incision infection and incision complete disruption were significantly lower (P<0.05) in the double-modified flap group and in the classical flap group. The incision maceration of the classical flap group was significantly higher than that of the interrupted suture group (P<0.05) or the double-modified flap group (P<0.05). No skin flap necrosis occurred in the double-modified flap group and the classical flap group. Conclusions Double-modified Limberg flap transplantation and classical Limberg flap transplantation have less complications and lower recurrence rate than interrupted suture after resection. Compare with classical Limberg flap transplantation, double-modified Limberg flap transplantation has a lower incision maceration rate. Because of limitation of sample size in this study, long-term clinical efficacy of double-modified Limberg flap transplantation needs to be confirmed by multicenter randomized controlled trials.