To compare the effect of skin flap plasty and minimally invasive resection in patients with facial pigmented nevus. Methods A total of 68 patients with facial pigmented nevus admitted to our hospital from June 2022 to June 2023 were selected as the research objects. According to the random number table method, they were divided into control group and observation group, with 34 patients in each group. The control group was treated with flap plasty, and the observation group was treated with minimally invasive resection. The clinical efficacy, adverse reactions and facial aesthetics of the two groups were compared. Results There was no significant difference in the total effective rate between the two groups (P >0.05). The incidence of adverse reactions in the observation group was 2.94%, which was lower than 17.65% in the control group (P <0.05). The overall facial beauty and skin color scores of the two groups after operation were higher than those before operation, and those in the observation group were higher than those in the control group (P <0.05). Conclusion Patients with facial pigmented nevus can achieve ideal results by skin flap plasty or minimally invasive resection, but minimally invasive resection has higher safety, lower risk of postoperative adverse reactions, and better facial aesthetics.