Objective To explore the efficacy and safety of fractional carbon dioxide laser in the treatment of patients with pigmented nevus. Methods A total of 70 patients with pigmented nevus admitted to our hospital from January 2023 to June 2024 were selected as the research subjects. According to the random number table method, they were divided into the control group and the study group, with 35 patients in each group. The control group received electroionization treatment, and the study group received fractional carbon dioxide laser treatment. The treatment effect, adverse reactions, wound healing time and wound pain degree were compared between the two groups. Results The total effective rate of treatment in the study group (97.14%) was higher than that in the control group (74.29%) (P <0.05). The incidence of adverse reactions in the study group (2.86%) was lower than that in the control group (20.00%) (P<0.05). The wound healing time in the study group was shorter than that in the control group, and the wound pain score in the study group was lower than that in the control group (P <0.05). Conclusion The application of fractional carbon dioxide laser in the treatment of patients with pigmented nevus has a good effect, which can effectively reduce the incidence of adverse reactions, help to shorten the wound healing time, and alleviate the degree of wound pain, with high efficacy and safety in treatment.