Objective Accurate prenatal diagnosis of congenital duodenal obstruction (CDO) is challenging. We aimed to determine new ultrasound metrics for accurate prenatal diagnosis of fetal CDO. Methods Data pertaining to 46 fetuses with suspected small intestinal obstruction (26 CDO; 16 high jejunal obstructions) were retrospectively analyzed. Prenatal ultrasonographic features including dilated intestinal length, stomach length, maximum intestinal dilatation, ratio of dilated intestinal length at late gestation and dilated stomach length (I/S ratio), and location of distal end of dilated bowel segment relative to spine were compared between CDO and high jejunal obstruction groups. The diagnostic performance of ultrasound indices was evaluated using receiver operating characteristics curve analysis. Results In 25 out of 26 CDO cases, the distal end of the dilated small intestine segment was located on the right side of spine, while that in the high jejunal obstruction group was located on the left side of spine. The dilated intestinal length and I/S ratio in CDO group were significantly smaller than those in high jejunal obstruction group (p < .05). Dilated intestinal length <51 mm or I/S ratio <1 showed high sensitivity (100, 100%) and specificity (96.1, 92.3%) for CDO (area under the curve: 0.995 and 0.988, respectively). There were no significant differences in the AUCs of dilated intestinal length and I/S ratio. Significant correlation of the site of obstruction in CDO with fetal dilated intestinal length and I/S ratio (r = 0.686; 0.660, p < .001, respectively) were noted. Conclusion Location of the distal end of the dilated small intestine segment relative to the spine, dilated intestinal length, and I/S ratio may help differentiate fetal CDO from high jejunal obstruction. The latter two metrics were associated with the site of obstruction in CDO patients.