The present study aimed to examine the association between discordant apolipoprotein B (Apo B) with low-density lipoprotein cholesterol (LDL-C) or non-high-density lipoprotein cholesterol (non-HDL-C) and cardiovascular disease (CVD) risk in the Chinese population and to determine whether adding information on Apo B to LDL-C and HDL-C improves CVD risk prediction. This study collected data from the China Health and Nutrition Survey from 2009 to 2015. Discordant Apo B with LDL-C and non-HDL-C were defined based on residual differences and medians. Logistic regression was used to examine the association between discordant Apo B with LDL-C or non-HDL-C and CVD risk. Areas under the receiver operating characteristic curve and categorical net reclassification improvement were utilized to assess the incremental predictive value of Apo B levels for CVD risk. A total of 7,117 participants were included, the mean age was 50.8 ± 14.3 years, 53.6% were female. During the 6-year follow-up, 207 CVD cases were identified. Participants with discordant high Apo B relative to LDL-C or non-HDL-C were at higher risk of CVD than those with the concordant group (odds ratio 1.38, 95% confidence interval 1.01 to 1.87; odds ratio 1.40, 95% confidence interval 1.01 to 1.94, respectively). However, Apo B had no significant contribution to the predictive value of the China atherosclerotic CVD (ASCVD) risk score (areas under the receiver operating characteristic curve 0.788 for China ASCVD score alone vs 0.790 for China ASCVD score plus Apo B). In conclusion, Apo B has the strongest association with CVD risk in healthy Chinese participants than LDL-C and non-HDL-C. However, it has minimal value in CVD risk assessment and discrimination.