To compare the image quality of magnetic resonance cholangiopancreatography (MRCP) in the supine position and prone position under the conditions of the same equipment, the same sequence (3D Navigator Triggered Sampling Perfection with Application-Optimized Contrast Using Different Flip-angle Evolutions, 3D-NT-SPACE) and the same patient, and to explore the clinical application value of prone position in MRCP examination to suppress respiratory motion artifacts. 53 participants who underwent MRCP in our hospital from April 2020 to August 2022 were prospectively collected. The 3D-NT-SPACE sequence was used in these patients. The visibility of the common bile duct, common hepatic duct, main pancreatic duct, and first- and second- and third-level branches of the intrahepatic bile duct and the comfort of the participants in two positions were subjective-evaluated. The Signal-to-noise ratio (SNR) and contrast-to-noise ratio were objective-evaluated. Statistical analysis was performed using Shapiro-Wilk, Levene's, Mann Whitney U test, Pearson chi-square test, and one-sample chi-square test. 53 patients (51.92years ± 2.02, 20 men) were evaluated. There were significant differences in the second- and third-level branches visibility score, the main pancreatic duct visibility score, the image quality score of the pancreaticobiliary tree, the blur and motion artifact score, the total image quality score, and SNR between the two positions (p < 0.05). The overall image quality of the prone position was better than that of the supine position. The prone position is a useful complement to the supine position.