Assessment of the presence of choledocholithiasis is crucial among acute biliary pancreatitis (ABP). Magnetic resonance cholangiopancreatography (MRCP) and endoscopic ultrasonography (EUS) are widely used to identify the gallstones of common bile duct (CBD). EUS provides better diagnostic accuracy and sensitivity than MRCP but carries a certain risk due to sedation. We investigated the risk factors of negative diagnosis of MRCP in ABP patients with choledocholithiasis for better selection of MRCP or EUS. A total of 2321 ABP patients were retrospectively included in this study. Based on the exclusion criteria, 337 ABP patients with negative MRCP results were ultimately included. Among these patients, 75 patients had positive EUS findings. Univariate and multivariate logistic regression models were used to screen the risk factors of negative diagnosis of MRCP in ABP patients with choledocholithiasis. Patients with positive EUS findings were older (62.0 vs. 55.0) and had higher rate of cholecystectomy history (18.7% vs. 7.3%) than those with negative EUS findings. The result of univariate logistic regression showed that the history of cholecystectomy, age and sex were potential risk factors (all p < 0.05). Then after adjusting the other potential risk factors (Direct bilirubin (DBIL), alanine transaminase (ALT), gamma-glutamyl transpeptidase (GGT) and alkaline phosphatase (ALP)), a history of cholecystectomy (OR = 2.859 [1.312,6.23]), older age (1.03 [1.009,1.052]) and male (2.016 [1.152,3.528]) were independent risk factors of negative diagnosis of MRCP in ABP patients with choledocholithiasis. The history of cholecystectomy, older age and male are independently associated with an increased risk of negative diagnosis of MRCP in ABP patients with choledocholithiasis. We suggest that patients with these risk factors should undergo EUS first, rather than MRCP.