Subtotal cholecystectomy (SC) is a useful procedure for avoiding bile duct injury in patients with difficult gallbladder. However, risk factors for conversion to SC, especially preoperative magnetic resonance cholangiopancreatography (MRCP) findings that predict conversion to SC, have not been investigated in detail. A total of 290 patients with acute cholecystitis who underwent laparoscopic cholecystectomy at our hospital between November 2011 and March 2020 were included. Patient characteristics and perioperative outcomes were reviewed, and preoperative clinical factors predicting conversion to SC were investigated. Forty-three patients underwent SC, whereas the remaining 247 patients underwent total cholecystectomy. An American Society of Anesthesiologists (ASA) score of 3 or greater (p = 0.011), surgery on or after 9days from symptom onset (p < 0.001), obscuration of the gallbladder wall around the neck on MRCP images (p = 0.010) and disruption of the common hepatic duct on MRCP images (p < 0.001) were significantly associated with conversion to SC. Logistic regression analyses revealed that an ASA score of 3 or greater (odds ratio = 2.667, p = 0.020), surgery on or after 9days from symptom onset (odds ratio = 4.229, p < 0.001) and disruption of the common hepatic duct on MRCP images (odds ratio = 4.478, p = 0.002) were independent predictors for conversion to SC. Early surgery yielded a lower risk for conversion to SC. Disruption of the common hepatic duct on preoperative MRCP images is associated with a risk for conversion to SC.