Objective To investigate the relations between blood lipid level, plasma atherogenic index and coronary artery structural changes in patients with subclinical coronary atherosclerosis. Method 209 patients who had accomplished Coronary CT Angiography (coronary CTA) are selected. the patients were classified into subclinical coronary atherosclerosis group (n = 124) and the normal group (n = 85). The clinical data of all patients were collected. Non-high-density lipoprotein, plasma atherogenic index, Castelli risk index and atherosclerosis coefficient were calculated according to the four items of blood lipids. Results There were significant differences between the subclinical coronary atherosclerosis group and the normal group in terms of gender, smoking history, and history of Hyperuricemia (P < 0.05), and the levels of Non-HDL-C, CRI-1, CRI-2, and AC were slightly higher than those in the normal group (P < 0.05).There was a correlation between subclinical coronary atherosclerosis and calcification score (P < 0.05). Logistic multivariate regression analysis showed that Smoking, Age and CRI-2 were independent risk factors for subclinical coronary atherosclerotic. The ROC of subclinical coronary atherosclerotic lesions diagnosed by CRI-2 was the largest, 0.611 (0.531–0.69). Conclusion Smoking, age and plasma CRI-2 level are associated with subclinical coronary atherosclerosis. CRI-2 in the plasma atherogenic index can be used for early screening of subclinical coronary atherosclerosis patients.