Objective To study the clinical effect of EnCor minimally invasive atherectomy in the treatment of benign breast tumor. Methods A total of 64 patients with benign breast tumors admitted to our hospital from March 2022 to March 2023 were selected as the research objects. They were divided into control group and observation group by random number table method, with 32 patients in each group. The control group was treated with traditional periareolar incision, and the observation group was treated with EnCor minimally invasive atherectomy. The treatment effect, clinical operation index, aesthetic appearance of breast, anxiety score and complications were compared between the two groups. Results The total effective rate of treatment in the observation group was 93.75%, which was higher than 81.25% in the control group (P <0.05). The intraoperative blood loss, operation time and wound healing time of the observation group were better than those of the control group (P <0.05). The scores of breast morphology, nipple areola sensation, wound scar and pigmentation in the observation group were higher than those in the control group (P <0.05). The GAD-7 score of the observation group was lower than that of the control group (P <0.05). The incidence of complications in the observation group was 9.38%, which was lower than 21.88% in the control group (P <0.05). Conclusion EnCor minimally invasive atherectomy is effective in the treatment of benign breast tumors. It has the characteristics of short operation time and rapid postoperative recovery. At the same time, it can reduce the patient's adverse emotions, improve the appearance of the postoperative breast appearance, and the risk of complications is low, which has good application effectiveness and safety.