Obesity-related metabolic disorders have not been adequately addressed due to a failure to distinguish the importance of general obesity or body fat distribution in relation to atherosclerotic risk factors, especially in the less obese populations. To assess the relationship between general obesity (reflected by BMI, total body fat percentage and total adiposity), body fat distribution (reflected by WHR, default regions and ROIs of DEXA) and atherosclerotic risk factors in the Chinese population, a total of 872 healthy subjects (477 male and 395 female) were enrolled in the study. The results indicated that the android pattern of fat distribution, independent of general obesity, was positively correlated with blood pressure, atherogenic indices, fasting and OGTT 2-h plasma glucose, glycosylated hemoglobin (HbA1c), serum concentration of cholesterol, triglyceride, LDL cholesterol and negatively correlated with HDL cholesterol in both genders. The gender differences in patterns of body fat distribution and atherosclerotic risk factors remained significant after adjustments were made for age, BMI and total adiposity, although diminished after further adjustments for body fat distribution. In conclusion, body fat distribution, rather than general obesity, is more correlated with obesity-related atherosclerotic risk factors and sex-associated differences. ROIs measured by DEXA may be a useful method to evaluate sex-associated changes in body fat distribution and atherosclerotic risk factors in the healthy Chinese population.