Objective To investigate the value of prenatal ultrasound and MRI in the diagnosis of types I and III fetal esophageal atresia (EA), in addition to analyzing the factors related to prognosis. Methods The clinical data regarding six cases of type I and 39 cases of type III EA, with the diagnosis confirmed by postnatal autopsy, MRI, CT, or surgical operation from November 2012 to January 2018, were retrospectively analyzed. Moreover, the prenatal ultrasound and MRI features were summarized. According to the prognosis, 45 fetuses with EA were divided into study (poor prognosis) and control (better prognosis) groups. Logistic regression was used to analyze the prognostic factors. Results The imaging features of 45 EA cases were as follows: Ultrasound features of fetal EA: polyhydramnios (AFI ≥ 25), continuously absent stomach bubble (rechecked 48 hours later), and reduced or no fetal swallowing over 30 minutes; the measured values for fetal head circumference (HC), abdominal circumference (AC), and estimated fetal weight (EFW) were lower than expected according to the clinical gestational age. MRI features: appearance of line-like long T1 and long T2 signals from the fetal neck to the esophagus at the upper mediastinal spinal anterior area; esophageal disconnection, sagging, or the appearance of a visible blind-ended pouch, and disappearance of the stomach bubble. Three cases (6.67%, 3/45) were diagnosed accurately by prenatal ultrasound, while 45 cases (100%, 45/45) were diagnosed accurately by MRI after prenatal ultrasound suggested EA. The incidences of complex cardiovascular malformation, low birth weight ( < 1200 g), EA type (type I), hypoproteinemia, and an esophageal deletion length > 5 cm were significantly higher in the poor prognosis group than those in the better prognosis group ( P < 0 05). Conclusions Due to interference factors such as fetal movement, excessive skin thickness, skeleton, and surrounding tissues and organs, only 6.67% of types I and III EA were directly diagnosed by prenatal ultrasound in the present study. The risk factors for poor prognosis of EA were complex cardiovascular malformation, low birth weight, EA type, hypoproteinemia, and esophageal deletion length > 5 cm; when these ultrasound features were found, performing MRI to diagnose EA and predict prognosis was valuable.