There are no appropriate variables for predicting postoperative morbidity in Crohn's disease (CD) patients with severe malnutrition. We examined a retrospective cohort to clarify these. Between 2005 and 2013, 138 CD patients with severe malnutrition underwent elective intestinal resection after preoperative management, consisting of nutritional support, abscess drainage, intravenous antibiotics, steroids tapering, and infliximab weaning, as appropriate. The severity of postoperative morbidity (within the first 30 days) was examined according to the Clavien-Dindo classification system. After a median duration of 26 days of preoperative management, Crohn's disease activity index (CDAI) and C-reactive protein (CRP) significantly decreased, and body mass index (BMI), skeletal muscle percentage (SMP), body fat percentage (BFP), albumin, prealbumin, and hemoglobin significantly increased (P < 0.001). Postoperative overall morbidities occurred in 28 (20.3 %) patients including 15 (10.8 %) major complications (Clavien-Dindo classification a parts per thousand yenaEuro parts per thousand III). In the multivariate logistic regression analysis, preoperative CRP (P = 0.044, OR 1.156, 95 % CI 1.004-1.331) was a significantly independent risk factor for overall complications, and preoperative SMP (P = 0.002, OR 0.487, 95 % CI 0.307-0.772) and BFP (P = 0.036, OR 0.691, 95 % CI 0.490-0.996) were significantly independent protective factors. Notably, only preoperative SMP (P = 0.002, OR 0.588, 95 % CI 0.422-0.820) was a significantly independent protective factor for major complications, and our threshold of SMP was 24.3 % (P < 0.001, sensitivity 83.7 %, specificity 95.9 %). Preoperative SMP is a protective factor for postoperative overall and major complications in CD patients with severe malnutrition and deserves further study.