To evaluate the impact of PM2.5 air pollution on atherogenic processes in modernizing Southern versus Northern China, we studied 1323 asymptomatic Chinese in Southern and Northern China in 1996–2007. PM2.5 exposure and metabolic syndrome (MS) were noted. Brachial flow-mediated dilation (endothelial function FMD) and carotid intima-media thickness (IMT) were measured by ultrasound. Although age and gender were similar, PM2.5 was higher in Northern China than in Southern China. The Northern Chinese were characterized by lower lipids, folate and vitamin B12, but higher age, blood pressures, MS and homocysteine (HC) (p = 0.0015). Brachial FMD was significantly lower and carotid IMT was significantly greater (0.68 ± 0.13) in Northern Chinese, compared with FMD and IMT (0.57 ± 0.13, p < 0.0001) in Southern Chinese. On multivariate regression, for the overall cohort, carotid IMT was significantly related to PM2.5, independent of location and traditional risk factors (Model R2 = 0.352, F = 27.1, p < 0.0001), while FMD was inversely related to gender, age, and northern location, but not to PM2.5. In Southern Chinese, brachial FMD was inversely correlated to PM2.5, independent of age, whereas carotid IMT was significantly related to PM2.5, independent of age and gender. In Northern Chinese, brachial FMD was inversely related to gender only, but not to PM2.5, while carotid IMT was related to traditional risk factors. Despite a higher PM2.5 pollution in Northern China, PM2.5 pollution was more significantly associated with atherogenic surrogates in Southern compared to Northern Chinese. This has potential implications for atherosclerosis prevention.