Objectives To retrospectively evaluate the diagnostic value of MRI for the uterotubal junctional pregnancies during the first trimester. Methods This retrospective study involved 59 patients (January 2016 to July 2021) with a preoperative imaging diagnosis of uterotubal junctional pregnancy. Using operative and pathological reports as the reference standard, we identified 22 patients with upper-lateral intracavitary (angular) pregnancy and 37 patients with interstitial pregnancy. Two senior radiologists, blinded to the patients' information, reviewed the MRI images and determined each MRI feature based on the original interpretation criteria. Any disagreement was resolved by discussion to achieve a consensus. The sensitivity and specificity of each MRI feature were calculated according to the reference standard. Results The endometrial thickness in the upper-lateral intracavitary pregnancy group was larger than in the interstitial group (p = 0.001). The cutoff value of the endometrial thickness was 11.5 mm with a sensitivity, specificity, and area under the curve that were 77.3%, 64.9%, and 0.743, respectively. Two key features to diagnose upper-lateral intracavitary pregnancy were "medial free edge" and "medial free edge plus above-cutoff endometrial thickness." The sensitivity and specificity of the medial free edge were 100% and 94.9%, respectively. The sensitivity and specificity of the medial free edge plus above-cutoff endometrial thickness were 77.3% and 100%, respectively. The key feature to diagnose interstitial pregnancy was an "intact lateral junctional zone," of which the sensitivity and specificity were 94.6% and 100%, respectively. Conclusions MRI can be used to differentiate the upper-lateral intracavitary pregnancy and interstitial pregnancy during the first trimester.