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Abstract Background To the best of our knowledge, no previous studies have explored the relationship between visceral obesity and malnutrition. Therefore, this study has aimed to investigate the association between them in patients with rectal cancer. Methods Patients with rectal cancer who underwent proctectomy were included. Malnutrition was defined according to the Global Leadership Initiative on Malnutrition (GLIM). Visceral obesity was measured using computed tomography (CT). The patients were classified into four groups according to the presence of malnutrition or visceral obesity. Univariate and multivariate logistic regression analyses were performed to evaluate risk factors for postoperative complications. Univariate and multivariate cox regression analyses were performed to evaluate the risk factors for overall survival (OS) and cancer-specific survival (CSS). Kaplan-Meier survival curves and log-rank tests were performed for the four groups. Results This study enrolled 624 patients. 204 (32.7%) patients were included in the well-nourished non-visceral obesity (WN) group, 264 (42.3%) patients were included in the well-nourished visceral obesity (WO) group, 114 (18.3%) patients were included in the malnourished non-visceral obesity (MN) group, and 42 (6.7%) patients were included in the malnourished visceral obesity (MO) group. In the multivariate logistic regression analysis, the Charlson comorbidity index (CCI), MN, and MO were associated with postoperative complications. In the multivariate cox regression analysis, age, American Society of Anesthesiologists (ASA) score, tumor differentiation, tumor node metastasis (TNM), and MO were associated with worsened OS and CSS. Conclusions This study demonstrated that the combination of visceral obesity and malnutrition resulted in higher postoperative complication and mortality rates and was a good indicator of poor prognosis in patients with rectal cancer.