Objective: Neophallic urethroplasty remains a significant challenge in penile reconstruction. Currently, there is no ideal recognized method. Through this article, we aimed to share our experiences of urethral reconstruction in the pedicled anterolateral thigh flap penile reconstruction using modified techniques and alternative flaps. Methods: In this single-center study from 2010 to 2020, 49 patients underwent penile reconstruction with a pedicled anterolateral thigh flap; 17 patients had a micropenis, 3 had iatrogenic defects, and 29 had penile defects after trauma. Different urethroplasty methods, complications, and revision methods were separately described. The tube-in-tube technique was used in 6 cases; the superficial iliac circumflex artery perforator (SCIAP) flap and pudendal-thigh flap were used in 26 and 11 cases, respectively, and the pedicled scrotal flap was used in 6 cases. Revision urethroplasty due to postoperative necrosis (n = 3), stricture (n = 8), and fistula (n = 2) were performed in 13 cases. Results: The urethral complications (flap necrosis, urinary fistula, and stricture) were as follows: tube-in-tube, 66.7%; SCIAP flap, 46.2%; pudendal-thigh flap, 38.5%; and scrotal septum flap, 50%. After revision procedures, all patients could urinate while standing. Conclusions: The characteristics and requirements of patients should be considered before designing a surgical plan. The tube-in-tube technique is the first choice for reconstructing the penis and urethra in a single stage for thinner patients. For other patients, a different flap can be used as a substitute for urethral reconstruction. The SCIAP, pudendal-thigh, and pedicled scrotal flaps can be used to reconstruct the urethra. The tubed SCIAP flap and pudendal-thigh flap are reliable, simple, and suitable for revision urethroplasty.