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Abstract Background Elderly patients undergoing cardiac operation often suffer various metabolic comorbidities, such as diabetes mellitus (DM) and obesity. The metabolic disorders in these individuals are widely considered to be possible predisposing factors for unfavourable prognosis. This retrospective study was aimed to determine the association of metabolic diseases with the mortality of elderly patients after coronary artery bypass grafting (CABG) and to identify the protective or risk factors related to their short- and long-term survival. Methods Totally 684 patients aged 75 years or above undergoing isolated CABG were evaluated retrospectively. There were two groups depending on the body mass index (BMI): an overweight and obesity group (n = 354) and a normal weight and lean group (n = 330). Propensity score matching (PSM) was performed to adjust baseline clinical characteristics, which reduced confounding bias. The short-term postoperative mortality was tested via logistic regression. Kaplan–Meier and Cox regression analyses were done to compute the overall survival in each group and to identify relevant variables associated with all-cause mortality, respectively. Results The prevalence rates of metabolic comorbidities in the total cohort were: diabetes mellitus (32.5%), overweight or obesity (51.8%) and hypertension (72.8%). The 30-day postoperative mortality was 5.1% and the long-term mortality was 15.25% at a median 46.2-month follow-up (1.0–178.6 months). The 30-day postoperative mortality was relevant to DM, diseased coronary arteries, New York Heart Association class, intra-aortic balloon pump and emergency surgery. The long-term mortality was negatively associated with overweight and obesity. Univariate and multivariate logistic regression recognized DM as an adverse factor related with 30-day postoperative mortality whether before or after PSM. The long-term mortality was not significantly relevant with DM (HR = 0.753, 95% CI 0.402–1.411). Overweight or obesity was not the risk factor of 30-day postoperative mortality (OR = 1.284, 95% CI 0.426–3.868), but was the protective factor of long-term survival (HR = 0.512, 95% CI 0.279–0.939). Conclusions The “obesity paradox” exists regarding the prognosis of individuals aged ≥ 75, which was presented as lower long-term mortality no matter from all cause or cardio-cerebrovascular cause in patients with BMI ≥ 24. Trial registration ChiCTR2200061869 (05/07/2022).