The relationship of cardiorespiratory fitness (CRF) with subclinical atherosclerosis affected by the body adiposity has been observed in children, whereas this relationship remains unclear in young adults. A total of 1520 military recruits, aged 18–40 years, were included in Taiwan in 2018–2020. All subjects underwent detailed physical and blood laboratory examinations. CRF was evaluated by time for a 3000 m run, and subclinical atherosclerosis was evaluated by intima–media thickness of the bulb of the left common carotid artery (cIMT) utilizing high-resolution ultrasonography. Multivariable linear regression analysis with adjustments for age, sex, cigarette smoking, alcohol intake, systolic and diastolic blood pressure, high- and low-density lipoprotein cholesterols, fasting glucose, waist circumference, serum uric acid and serum triglycerides were utilized to determine the correlation between CRF and cIMT. CRF was independently correlated with cIMT (standardized β: 0.11, p < 0.001). Of the cardiometabolic risk markers, serum triglycerides were the only independent risk marker of cIMT (standardized β: 0.063, p = 0.03). In addition, the association of CRF with cIMT did not differ between those with a body mass index (BMI) ≥ 25 kg/m² and those with BMI < 25 kg/m² (standardized β: 0.103 and 0.117; p = 0.01 and 0.005, respectively). In physically active young men and women, there was an inverse association of cIMT with CRF, which was observed in both overweight/mild obesity and normal-weight individuals, highlighting the importance of endurance capacity on reducing risk of early atherosclerosis and implying that the moderation effect of body adiposity might not be present in this population.