Objective To explore the risk factors of persistent ectopic pregnancy (PEP) in patients with fallopian tubal pregnancy after tubal pregnancy surgery. Methods A total of 38 patients, who underwent the tubal pregnancy surgery in International Peace Maternity and Child Health Hospital affiliated to Medical College of Shanghai Jiao Tong University from January 2000 to December 2020, were selected as the research subjects and included into PEP group; and another 152 patients undergone the same operation during the same period and recovered well were selected as control group. The clinical data of the two groups were analyzed retrospectively. The age, gravidity, body mass index (BMI), menopause duration, previous fallopian tube surgery history, postoperative serum β-human chorionic gonadotropin (β-HCG) decline rate, tubal pregnancy site, ectopic pregnancy focus, and intraoperative pelvic adhesion etc. of all patients were recorded and analyzed. The clinical baseline data of the two groups were analyzed. The chi square test was used to analyze the risk factors of PEP after tubal pregnancy surgery, and Poisson regression analysis was performed to do the multivariate analysis. The independent risk factors of PEP after tubal pregnancy surgery were screened, and then the treatment method of PEP after tubal pregnancy surgery was analyzed. Results There were no significant differences between PEP group and control group in terms of age, gravidity, BMI and menopause duration. Univariate analysis showed that the PEP after tubal pregnancy surgery was related to emergency/elective surgery, pelvic adhesion and the rupture of ectopic pregnancy lesions/abortion, and the difference was statistically significant (P<0.05), while no obvious relation to the operation method, the location of tubal pregnancy and the size of ectopic pregnancy focus. Poisson regression analysis showed that the pelvic adhesion and the rupture of ectopic pregnancy lesions/abortion were the independent risk factors of PEP. The cure rates with methotrexate (MTX) treatment was 95% for PEP patient after tubal pregnancy surgery. Conclusion The pelvic adhesion and the rupture of ectopic pregnancy lesions/abortion were the independent risk factors of PEP after the tubal pregnancy surgery.