Objective To explore efficacy and safety of compound polymyxin B ointment combined with fractional laser in the treatment of acne scars. Methods A total of 60 patients with acne scars admitted to the Department of Dermatology and Venereology, Huai’an First People’s Hospital from May 2022 to May 2023 were selected as the research subjects, and they were divided into control group and observation group by the random number table method, with 30 patients in each group. The control group was treated with fractional laser, and the observation group was treated with compound polymyxin B ointment and fractional laser. The acne basal depth, therapeutic effect, ECCA, skin lesion score, skin condition changes and adverse reaction rate were compared between the two groups. Results After 30 and 90 days of treatment, the basal depth of acne in the observation group was lower than that in the control group (P <0.05). The total effective rate of treatment in the observation group (96.67%) was higher than that in the control group (66.67%) (P <0.05). After treatment, the scores of ECCA and skin lesion in the observation group were lower than those in the control group (P <0.05). The decrustation time, swelling disappearance time and pain disappearance time in the observation group were shorter than those in the control group (P <0.05). There was no significant difference in the incidence of adverse reactions between the two groups (P >0.05). Conclusion The combination of compound polymyxin B ointment and fractional laser in the treatment of acne scars is safe and effective, and can reduce the degree of skin lesions and scars, which is worthy of application.