Achieving optimal nutritional status in patients with penetrating Crohn’s disease (CD) is crucial in preparing for surgical resection. However, there is a dearth of literature comparing the efficacy of total parenteral nutrition (TPN) versus exclusive enteral nutrition (EEN) in optimizing postoperative outcomes. Hence, we conducted a case-matched study to assess the impact of preoperative EEN versus TPN on the incidence of postoperative adverse outcomes, encompassing overall postoperative morbidity and stoma formation, among penetrating CD patients undergoing bowel surgery. From December 1, 2012 to December 1, 2021, a retrospective study was conducted at a tertiary center to enroll consecutive patients with penetrating CD who underwent surgical resection. Propensity score matching (PSM) was utilized to compare the incidence of postoperative adverse outcomes. Furthermore, univariate and multivariate logistic regression analyses were conducted to identify the risk factors associated with adverse outcomes. The study included 510 patients meeting the criteria. Among them, 101 patients in the TPN group showed significant improvements in laboratory indicators at the time of surgery compared to pre-optimization levels. After matching, TPN was increased occurrence of postoperative adverse outcomes (92.2% vs. 64.1%, p = 0.001) when compared to EEN group. In the multivariate analysis, TPN showed a significantly higher odds ratio for adverse outcomes than EEN (OR = 4.241; 95% CI 1.567-11.478; p = 0.004). The study revealed that penetrating CD patients who were able to fulfill their nutritional requirements through EEN exhibited superior nutritional and surgical outcomes in comparison to those who received TPN.