Objective To compare the clinical effects of high intensity focused ultrasound (HIFU) ablation and laparoscopic focal resection in the treatment of focal adenomyosis (FAM). Methods A retrospective analysis was conducted on the clinical data of 120 patients with FAM. Among them, 60 patients who received laparoscopic focal resection were designed as the control group, and 60 patients who received HIFU ablation during the same period were designed as the observation group. Surgical indicators (operation time, postoperative hospital stay and postoperative recovery time) were compared between the two groups. The degree of dysmenorrhea (pain visual analogue scale [VAS] score) and menstrual volume (pictorial blood loss assessment chart [PBAC] score) were compared between the two groups before surgery, 3 months after surgery and 6 months after surgery. The quality of life (scores of WHO Quality of Life-BREF [physiological, psychological, social and environmental domains]) was compared between the two groups before surgery and 6 months after surgery. The recurrence rate and occurrence of complications were compared between the two groups during the 2-year postoperative follow-up. Results The operation time, postoperative hospital stay and postoperative recovery time were shorter in the observation group than in the control group (P<0.05). At 3 months after surgery, the pain VAS scores and PBAC scores in both groups were decreased compared with preoperative values, and those in the observation group were lower than in the control group (P<0.05). At 6 months after surgery, the pain VAS scores and PBAC scores in both groups were decreased compared with preoperative and 3-month postoperative values, and those in the observation group were lower than in the control group (P<0.05). At 6 months after surgery, the physiological, psychological, social and environmental domain scores in both groups were higher than preoperative scores, and those in the observation group were higher than in the control group (P<0.05). There were no statistically significant differences in the recurrence rate and overall complication rate between the two groups (P>0.05). Conclusion HIFU ablation is superior to laparoscopic focal resection in lesion ablation, dysmenorrhea relief and menstrual blood loss reduction, and is more conducive to postoperative rehabilitation and fundamental improvement of quality of life in patients with FAM.