This study aimed to investigate application of Onodera prognostic nutrition index (OPNI) and neutrophil-to-lymphocyte ratio (NLR) in evaluating risk of postoperative complications in Crohn's disease (CD). Clinical data of 108 postoperative CD patients in 9 years were respectively reviewed. OPNI and NLR were within 1 week preoperatively. Average OPNI was 38.8 ± 8.2 and significantly lower in patients with: CD type B3; lymphopenia; decreased haemoglobin, prealbumin, and albumin; and daily enteral nutrition <500 kcal/d. Average NLR was 5.9 ± 12.1 and significantly higher in patients with: CD type B3, neutrophilia, lymphopenia, decreased prealbumin, and enteral nutrition <500 kcal/d. Youden index was maximal at OPNI 39.8 and NLR 4.1, patients were divided into two groups by OPNI 39.8 and NLR 4.1; Low OPNI (≤39.8) group had significantly greater incidence of type B3, lymphopenia, decreased haemoglobin, prealbumin and albumin, and enteral nutrition <500 kcal/day, more likely to have intra-abdominal bleeding. High NLR group (≥4.1) had significantly greater incidence of type B3, neutrophilia, and lymphopenia, more likely to develop lung infection. OPNI and NLR were significantly negatively correlated. Smoking within 1 year preoperatively, OPNI <39.8, NLR ≥ 4.1 were independent risk factors for postoperative complications in CD.