Objective: Individuals without conventional cardiovascular risks (CVRFs) still have the risk of adverse outcomes, and subclinical carotid atherosclerosis is a known predictor of cardiovascular events. We aimed to assess the prevalence and associated risk factors of subclinical carotid atherosclerosis in CVRF-free population. Methods: The cross-sectional study was conducted in rural northeast China in 2017-2018. CVRFs freedom was defined as untreated blood pressure < 140/90 mmHg, fasting plasma glucose < 7.0 mmol/L, untreated total cholesterol < 6.22 mmol/L, low-density lipoprotein cholesterol < 4.14 mmol/L, high-density lipoprotein cholesterol (HDL-C) ≥ 1.04 mmol/L, and no current smoking. This subgroup population included 1449 individuals, and ultrasound was used to detect carotid atherosclerosis. Results: The mean carotid intima-media thickness is 0.74 ± 0.14 mm. The prevalence of carotid plaque is 23.4% (95%CI: 21.2%-25.6%) among CVRFs-free population, significantly higher in men than in women (37.1% vs 20.0%, p<0.001), and rises steeply with advancing age. 1.31% have moderate-to-severe carotid stenosis. Advancing age, man, glycosylated hemoglobin (OR, 1.90; 95% CI, 1.20-1.32), HDL-C level (OR, 2.31; 95% CI, 1.75-3.04), and pulse pressure (OR, 1.03; 95% CI, 1.01-1.05) are potentially related to presence of carotid atherosclerosis. Adjusted-dose-response association shows a linear relationship between HDL-C and prevalence of carotid atherosclerosis. Conclusions: The prevalence of subclinical carotid atherosclerosis in CVRF-free population was relatively high, indicating poorly defined factors might contribute to the early atherogenesis. Moreover, we observed a paradoxical response between subclinical carotid atherosclerosis and HDL-C levels, suggesting that treatment targeting to increase HDL-C levels might not reduce future cardiovascular risks.