Background Treatment of congenital hemivertebra is challenging and data on long-term follow-up (>= 5 years) are lacking. This study evaluated the surgical outcomes of posterior thoracolumbar hemivertebra resection and short-segment fusion with pedicle screw fixation for treatment of congenital scoliosis with over 5-year follow-up. Methods This study evaluated 27 consecutive patients with congenital scoliosis who underwent posterior thoracolumbar hemivertebra resection and short-segment fusion from January 2007 to January 2015. Segmental scoliosis, total main scoliosis, compensatory cranial curve, compensatory caudal curve, trunk shift, shoulder balance, segmental kyphosis, and sagittal balance were measured on radiographs. Radiographic outcomes and all intraoperative and postoperative complications were recorded. Results The segmental main curve was 40.35 degrees preoperatively, 11.94 degrees postoperatively, and 13.24 degrees at final follow-up, with an average correction of 65.9%. The total main curve was 43.39 degrees preoperatively, 14.13 degrees postoperatively, and 16.06 degrees at final follow-up, with an average correction of 60.2%. The caudal and cranial compensatory curves were corrected from 15.78 degrees and 13.21 degrees to 3.57 degrees and 6.83 degrees postoperatively and 4.38 degrees and 7.65 degrees at final follow-up, with an average correction of 69.2% and 30.3%, respectively. The segmental kyphosis was corrected from 34.30 degrees to 15.88 degrees postoperatively and 15.12 degrees at final follow-up, with an average correction of 61.9%. A significant correction (p < 0.001) in segmental scoliosis, total main curve, caudal compensatory curves and segmental kyphosis was observed from preoperative to the final follow-up. The correction in the compensatory cranial curve was significant between preoperative and postoperative and 2-year follow-up (p < 0.001), but a statistically significant difference was not observed between the preoperative and final follow-up (p > 0.001). There were two implant migrations, two postoperative curve progressions, five cases of proximal junctional kyphosis, and four cases of adding-on phenomena. Conclusion Posterior thoracolumbar hemivertebra resection after short-segment fusion with pedicle screw fixation in congenital scoliosis is a safe and effective method for treatment and can achieve rigid fixation and deformity correction.