Background: Metabolically unhealthy obesity (MUO) has been associated with surface electrocardiographic (ECG) left ventricular hypertrophy (LVH), left atrial enlargement (LAE), and inferior T wave inversions (TWI) in the middle- and old-aged populations. However, the relationship between obesity phenotypes and these ECG abnormalities in physically active young adults is yet to be determined.Methods: A total of 2,156 physically active military males aged 18–50 in Taiwan were analyzed. Obesity and metabolically unhealthy status were, respectively, defined as the body mass index ≥27 kg/m2 and the presence of metabolic syndrome based on the ATPIII criteria for Asian male adults. Four groups were classified as the metabolically healthy non-obesity (MHNO, n = 1,484), metabolically unhealthy non-obesity (MUNO, n = 86), metabolically healthy obesity (MHO, n = 376), and MUO (n = 210). ECG-LVH was based on the Sokolow–Lyon and Cornell voltage criteria, ECG-LAE was defined as a notched P wave ≥0.12 s in lead II or a notch of ≥0.04 s, and inferior TWI was defined as one negative T wave axis in limb leads II, III, or aVF. Physical performance was evaluated by time for a 3-km run. Multiple logistic regression analysis with adjustment for age, smoking, alcohol drinking, and physical performance was utilized to investigate the associations between obesity phenotypes and the ECG abnormalities.Results: As compared to MHNO, MUNO, MHO, and MUO were associated with lower risk of Sokolow–Lyon-based ECG-LVH [odds ratios (OR) and 95% confidence intervals: 0.80 (0.51–1.25), 0.46 (0.36–0.58), and 0.39 (0.28–0.53), respectively; p for trend <0.001], and with greater risk of ECG-LAE [OR: 0.87 (0.44–1.72), 2.34 (1.77–3.10), and 3.02 (2.13–4.28), respectively; p for trend <0.001] and inferior TWI [OR: 2.21 (0.74–6.58), 3.49 (1.97–6.19), and 4.52 (2.38–8.60), respectively; p for trend <0.001]. However, no associations between obesity phenotypes and Cornell-based ECG-LVH were found.Conclusion: In physically active young males, obesity was associated with higher risk of ECG-LAE and inferior TWI, whereas the risk between obesity and ECG-LVH might vary by the ECG criteria, possibly due to a high prevalence of exercise induced-LVH in military and greater chest wall thickness in obesity. The cardiovascular prognosis of ECG-LVH in physically active obese adults requires further study.