Objective To investigate the clinical effect of autologous hair unit transplantation by microsurgical technique in the treatment of hair loss. Methods A total of 76 patients with hair loss admitted to our hospital from March 2022 to November 2023 were selected as the research objects. They were divided into control group and observation group by random number table method, with 38 patients in each group. The control group was treated with traditional transplantationsurgery, and the observation group was treated with microsurgery for autologous hair unit transplantation. The transplantation survival, aesthetic effect, complications and satisfaction of the two groups were compared. Results The excellent and good rate of transplantation survival in the observation group was 94.74%, which was higher than 71.05% in the control group (P <0.05). The excellent and good rate of aesthetic hair transplantation in the observation group was 97.37%, which was higher than 73.68% in the control group (P <0.05). The incidence of complications in the observation group was 13.15%, which was lower than 36.84% in the control group (P <0.05). The satisfaction score of the observation group was higher than that of the control group (P <0.05). Conclusion Microsurgical technique for autologous hair unit transplantation is effective in the treatment of hair loss, which can improve the survival rate of hair grafting, improve the aesthetics degree of hair transplantation, improve patient satisfaction, and reduce the risk of postoperative complications. It is worthy of clinical application.