ObjectiveTo investigate the effectiveness of penile up transfer method in the treatment of penoscrotal transposition (PST) in children. Methods A clinical data of 46 children with PST admitted between January 2015 and March 2021 and met selective criteria was retrospectively analyzed. The M-shaped scrotal flap method was adopted in 21 cases (group A), and the penile up transfer method was adopted in 25 cases (group B). There was no significant difference in age and PST typing between the two groups (t=0.491, P=0.626; χ2=0.710, P=0.790). The operation time and postoperative complications of the two groups were recorded and compared, and the correction effect of PST was evaluated. Results All operations were successfully completed, and no urethral injury occurred during operation. The operation time was significantly less in group B than in group A [(70.36±9.76) minutes vs. (96.62±13.18) minutes; t=7.553, P=0.000]. All children were followed up 6-33 months (mean, 13.2 months). There were 5 cases (23.8%) of skin necrosis and 6 cases (28.6%) of scar hyperplasia in group A, and 1 case (4.0%) of skin necrosis and 1 case (4.0%) of scar hyperplasia in group B. The incidence of complication was significantly lower in group B than in group A (χ2=3.949, P=0.047; χ2=5.341, P=0.021). In the evaluation of PST correction at 6 months after operation, there were 15 cases of complete correction and 6 cases of incomplete correction in group A, 24 cases of complete correction and 1 case of incomplete correction in group B, and the difference was significant (χ2=5.341, P=0.021). Conclusion The penis up transfer method is not only easy to correct PST, but also can correct scrotal separation at the same time, with fewer postoperative complications and satisfactory correction effect of penile scrotal appearance.