Abstract Background Coronary atherosclerosis can lead to serious cardiovascular events. In type 2 diabetes (T2DM) patients, the effects of clinical factors on coronary atherosclerosis have not been fully elucidated. We used a clustering method to distinguish the population heterogeneity of T2DM and the differences in coronary atherosclerosis evaluated on coronary computed tomography angiography (CCTA) among groups and to facilitate clinical management. Methods Clinical data from 1157 T2DM patients with coronary atherosclerosis who underwent CCTA in our hospital from January 2018 to September 2021 were retrospectively collected. The coronary artery segment plaque type and stenosis, the number of involved vessels, the segment involvement score (SIS) and the segment stenosis score (SSS) were evaluated and calculated. Unsupervised clustering analysis based on clinical information was used (cluster 1: n = 463; cluster 2: n = 341; cluster 3: n = 353). The association of coronary plaque characteristics with cluster groups was evaluated. Results The clinical data among the three groups were different in several aspects: (1) Cluster 1 had the least male patients (41.7%), the lowest proportion of patients with smoking (0%) or alcohol history (0.9%), and the lowest level of serum creatinine (74.46 ± 22.18 µmol/L); (2) Cluster 2 had the shortest duration of diabetes (7.90 ± 8.20 years) and was less likely to be treated with diabetes (42.2%) or statins (17.6%) and (3) Cluster 3 was the youngest (65.89 ± 10.15 years old) and had the highest proportion of male patients (96.6%), the highest proportion of patients with smoking (91.2%) and alcohol (59.8%) history, the highest level of eGFR (83.81 ± 19.06 ml/min/1.73m²), and the lowest level of HDL-C (1.07 ± 0.28 mmol/L). The CCTA characteristics varied with different clusters: (1) Cluster 1 had the largest number of segments with calcified plaques (2.43 ± 2.46) and the least number of segments with mixed plaques (2.24 ± 2.59) and obstructive stenosis (0.98 ± 2.00); (2) Cluster 1 had the lowest proportion of patients with mixed plaques (68%) and obstructive stenosis (32.2%); (3) Cluster 3 had more segments with noncalcified plaques than cluster 1 (0.63 ± 1.02 vs 0.40 ± 0.78, P < 0.05) and the highest proportion of patients with noncalcified plaques (39.9%) and (4) There was no significant difference in the extent of coronary plaques among the three clusters. Conclusions The unsupervised clustering method could address T2DM patients with heterogeneous clinical indicators and identify groups with different types of coronary plaque and degrees of coronary stenosis. This method has the potential for patient stratification, which is essential for the clinical management of T2DM patients with coronary atherosclerosis.