Background Intramural ectopic pregnancy（IMP）is an uncommon type of ectopic pregnancy and can be life-threatening if misdiagnosed. Thus, early diagnosis and management are required. However, due to its rarity, there was no suggested algorithm for this rare disorder. Methods We conducted a case-control study and discuss multiple treatments and risk factors of IMP. Chi-square test, contingency table methods and logistic regression analysis were used to evaluate. Results Only 2.4% of patients have a low level of serum human chorionic gonadotropin (HCG) (less than 10mIU/ml). 184(73.02%) of patients have been misdiagnosed. The rate of accurate initial diagnosis may be increased using Magnetic resonance imaging (MRI). The majority of patients underwent surgery (89.68%). Approximately one-tenth of patients can be successfully treated by pharmacotherapy. The history of dilatation and curettage (OR = 4.42 95% CI 2.97-6.59, P＜0.001), history of tubal surgery (OR = 4.17 95% CI 2.27-7.68 P< 0.001), cesarean section (OR = 5.66 95% CI 1.99-16.05 P=0.001) and intrauterine devices (IUD)(OR = 6.04 95% CI 2.46-14.80 P< 0.001) were significant risk factors for IMP. Conclusion Patients at gestation age should be evaluated thoroughly even with the normal HCG level, to avoid a delayed diagnosis of pregnancy-related disorders like IMP. Diagnosis may be increased using MRI and Contrast-enhanced ultrasound (CEUS). After a thorough evaluation, drug therapy can be a treatment choice; however, conservative surgery appears safer and more effective. Risk factors should be comprehensively considered to help to reduce the incidence of IMP and to increase diagnosis rate.