To investigate the clinical effect of autologous bone and nasal alar rotation flap reconstruction in the treatment of nasal alar invagination. Methods A total of 68 patients with nasal alar retraction admitted to our hospital from February 2020 to February 2022 were selected as the research objects. They were divided into control group and study group by random number table method, with 34 patients in each group. The control group was treated with silicone material combined with nasal alar rotation flap for reconstruction. The study group was treated with autologous bone combined with nasal alar rotation flap for reconstruction. The nostril measurement index, nasal alar correction degree, facial beauty satisfaction, psychological state and complications were compared between the two groups. Results After treatment, the transverse diameter of the nostrils in the study group was smaller than that in the control group, and the longitudinal diameter of the nostrils was larger than that in the control group (P <0.05). After treatment, the distance between nasal alar baseline and facial midline in the study group was less than that in the control group, and the height of nasal ridge was higher than that in the control group (P <0.05) The satisfaction rate of facial beauty in the study group was higher than that in the control group (P <0.05). After treatment, the SCL-90 score of the study group was lower than that of the control group (P <0.05). The incidence of postoperative complications in the study group was 5.88%, which was lower than 26.47% in the control group (P <0.05). Conclusion Autologous bone and nasal alar rotation flap for reconstruction can achieve ideal results in the treatment of nasal alar invagination, which can promote the recovery of nostril diameter, improve the correction effect of nasal alar, improve the facial beauty satisfaction of patients, and regulate their psychological state. Meanwhile, the risk of complications is low and the safety is high.