Metabolically healthy obese (MHO) individuals generally show better cardiovascular prognosis compared with metabolically unhealthy counterparts, which may be related to different patterns of target organ damage (TOD). We aimed to investigate the patterns of TOD related to obesity and metabolic unhealthiness. A total of 659 Korean adults (mean age, 60.0 ± 11.8 years; male, 51.1%) undergoing health examinations were stratified into four groups according to obesity (body mass index ≥25.0 kg/m2) and metabolic healthiness (meeting ≤1 criteria of metabolic syndrome excluding abdominal circumference): metabolically healthy nonobese (MHNO), metabolically unhealthy nonobese (MUNO), MHO, and metabolically unhealthy obese (MUO). Four measures of TOD were evaluated: arterial stiffness, renal dysfunction, left ventricular (LV) diastolic dysfunction, and LV hypertrophy (LVH). In multivariable analyses, compared with the MHNO group, the MHO group showed 2.31 times higher odds for LVH, whereas, the MUNO group showed 3.14 and 6.28 times higher odds for increased arterial stiffness and renal dysfunction, respectively. Metabolic unhealthiness was associated with increased arterial stiffness [odds ratio (OR) 2.73; confidence interval (95% CI) 1.72-4.34], renal dysfunction (OR 4.02; 95% CI 1.54-10.49), and LV diastolic dysfunction (OR 2.28; 95% CI 1.14-4.55). Meanwhile, obesity showed weaker association with LVH and LV diastolic dysfunction, and was not associated with increased arterial stiffness and renal dysfunction in multivariable analyses. Metabolic unhealthiness shows more association with TOD than obesity, which may contribute to the higher risk of cardiometabolic abnormalities in MUNO compared with MHO.