BACKGROUND: A majority of factors associated with the occurrence of clinical relevant postoperative pancreatic fistula (CR-POPF) after pancreaticoduodenectomy (PD) can only be identified intra- or postoperatively. There are no reports for assessing the morphological features of pancreatic stump and analyzing its influence on CR-POPF risk after PD preoperatively. METHOD: A total of 90 patients underwent PD between April 2012 and May 2014 in our hospital were included. Preoperative computed tomographic (CT) images were imported into the Medical Image Three-Dimensional Visualization System (MI-3DVS) for acquiring the morphological features of pancreatic stump. The demographics, laboratory test and morphological features of pancreatic stump were recorded prospectively. The clinical course was evaluated focusing on the occurrence of pancreatic fistula as defined by the International Study Group on Pancreatic Fistula (ISGPF). Logistic regression analysis was used to identify independent predictors of CR-POPF. RESULTS: CR-POPF occurred in 18 patients (14 grade B, 4 grade C). In univariate analysis, male gender (P = 0.026), body mass index (BMI) ≥ 25.3 kg/m(2) (P = 0.002), main pancreas duct diameter (MPDD) < 3.1 mm (P = 0.005), remnant pancreatic parenchymal volume (RPPV) > 27.8 mL (P < 0.001), and area of cut surface (AOCS) > 222.3 mm(2) (P < 0.001) were associated with an increased risk of CR-POPF. In multivariate analysis, BMI ≥ 25.3 kg/m(2) (OR 12.238, 95 % CI 1.822-82.215, P = 0.010) and RPPV > 27.8 mL (OR 12.907, 95 % CI 1.602-104.004, P = 0.016) were the only independent risk factors associated with CR-POPF. A cut-off value of 27.8 mL for RPPV established based on the receiver operating characteristic (ROC) curve, which was the strongest single predictive factor for CR-POPF, with a sensitivity and specificity of 77.8 and 86.1 %, respectively. The area under the ROC curve of RPPV was 0.770 (95 % CI 0.629-0.911, P < 0.001). CONCLUSIONS: Our study demonstrated that CR-POPF is correlated with BMI and RRPV. MI-3DVS provides us a novel and convenient method for measuring the RPPV. Preoperative acquisition of RPPV and BMI may help the surgeons in fitting postoperative management to patient's individual risk after PD.