Different blood pressure (BP) indices had varying associations with carotid intima-media thickness (cIMT) and plaques in clinical practice. However, insufficient evidence has focused on this issue, especially in Chinese population. Herein we examined associations of different BP indices with cIMT and plaques cross-sectionally in a community-based atherosclerosis cohort. We qualitatively measured cIMT and plaques, and also measured central systolic blood pressure and brachial systolic blood pressure (baSBP), from which pulse pressure (PP), and second PP (PP2) were calculated. Logistic multivariate regression was used to assess the associations with BP indices and carotid artery hypertrophy (increased cIMT) and the extent of atherosclerosis (presence of plaques). Each BP index was significantly and independently associated with increased cIMT and plaques except the association of baSBP with plaques. When every two BP indices were put into one model, brachial pressure indices were associated with increased cIMT independently of central pressures, whereas the association between central pressure indices and plaque presence were stronger than those of brachial pressures. In addition, SBP indices were associated with increased cIMT independently of PP indices, whereas PP indices were more strongly related to plaques. In conclusion, central and PP indices might be associated with plaques; however, brachial and SBP indices might be associated with increased cIMT. Nevertheless, whether these BP indices predict increased cIMT and plaque progression warrants further longitudinal and laboratory studies.