Objective To investigate the clinical effect of high intensity focused ultrasound (HIFU) and uterine artery embolization (UAE) in the treatment of cesarean scar pregnancy (CSP). Methods A total of 152 patients with CSP diagnosed by B-type ultrasonography were enrolled prospectively in this study from June 2014 to May 2016 in Chengdu Women and Children’s Central Hospital and Suining Central Hospital. Six patients from Chengdu Women and Children’s Central Hospital and 84 from Suining Central Hospital for Volunteered HIFU treatment were regarded as observation group. The other 62 patients from Chengdu Women and Children’s Central Hospital were selected to accept UAE treatment voluntarily were designated as control group. The clinical efficacy and therapeutic safety of the two groups were compared after the treatment. Results Eighty-two patients (91.1%) in the observation group and 32 (51.6%) in the control group had a bleeding volume equal to 100 mL or lower during complete curettage of uterine cavity (P<0.05). The hospitalization expenses of the above two groups were respectively (25 126.51±1 473.49) and (32 928.42 ±1 579.35) yuan (P<0.05). The hospitalization time was (11.03±1.52) and (10.65±1.87) days respectively, and the difference was not statistically significant (P>0.05). There was no significant difference in the normal rate of human chorionic gonadotropin recovery between the observation group and the control group at 14 days after treatment (P>0.05). Eighty-seven patients (96.7%) in the observation group and 51 (82.3%) in the control group had their menstrual recovery to normal level at 2 months after treatment, and the difference was statistically significant (P<0.05). The incidence of postoperative complications was 1.1% and 6.4% in the observation group and the control group, respectively, and the difference was not statistically significant (P>0.05). Conclusions HIFU in the treatment of CSP is safe and effective. Compared with UAE, HIFU requires less cost with fewer complications, which is worth promoting.