High level of apolipoprotein B (Apo B) is associated with incident subclinical atherosclerosis. The present study evaluated the associations between discordant Apo B with low-density lipoprotein cholesterol (LDL-C), non-high-density lipoprotein cholesterol (non-HDL-C), and coronary atherosclerotic burden. This study enrolled 3043 participants aged 50-75 years from the PolyvasculaR Evaluation for Cognitive Impairment and vaScular Events (PRECISE) study that was conducted in the community in Lishui City, China. Discordant Apo B with LDL-C and non-HDL-C were defined by residuals and medians. Coronary atherosclerotic burden was evaluated by segment involvement score (SIS) and segment stenosis score (SSS) which were determined by computed tomography angiography. We performed discordance analyses examining associations of discordant Apo B with LDL-C or non-HDL-C with the coronary atherosclerotic burden. The mean age of participants was 61.2 ± 6.7 years, 53.6% were females. Participants with discordant high Apo B relative to non-HDL-C were at higher odds of plaques [odds ratio (OR), 1.30; 95% confidence interval (CI), 1.08-1.57], SIS [common odds ratio (cOR), 1.35; 95% CI, 1.14-1.60], and SSS (cOR, 1.40; 95% CI, 1.18-1.67) compared with concordant group. However, discordantly low Apo B with non-HDL-C was associated with decreased odds of the coronary atherosclerotic plaques and its burden. Similar results were shown for discordant analyses for Apo B with LDL-C. Discordantly high Apo B with LDL-C and non-HDL-C were associated with an increased odds of the coronary atherosclerotic plaques and its burden. These findings highlighted the importance of Apo B for primary prevention of coronary atherosclerosis.