The study investigated the potential association among pancreatitis, pancreas divisum (PD), and santorinicele or wirsungocele (two types of pancreatic ductal variations) based on three-dimensional magnetic resonance cholangiopancreatography (3D-MRCP). The clinical and imaging samples of 75 patients were collected and sorted into santorinicele and wirsungocele groups. Potential factors related to wirsungocele and santorinicele were investigated. MRCP showed good performance in visualizing ductal anomalies. Patients with santorinicele had higher risks of developing pancreatitis compared with those with wirsungocele. Additionally, santorinicele itself might be more closely associated with pancreatitis than with PD.