Objectives: Ankylosing spondylitis (AS) is an autoinflammatory, chronic disease. Patients with AS are at increased risk of cardiovascular disease (CVD). The link between AS and subclinical atherosclerosis is multifactorial and still not completely understood. The aim of this study was to examine the potential associations between carotid intima–media thickness (cIMT) and different cardiometabolic biomarkers in individuals with AS. Methods: A total of 96 patients with AS were prospectively included. cIMT was measured via ultrasonography. Multiple linear regression analysis was used to find the best predictors of cIMT values. Principal component analysis (PCA) was implemented to extract factors that were further tested via binary logistic regression analysis in relation to cIMT. Results: Waist circumference (WC), low-density lipoprotein cholesterol (LDL-c), and the BASDAI score were independently correlated with cIMT in AS patients (p = 0.037, p = 0.060, and p = 0.048, respectively; adjusted R2 = 0.113). PCA extracted four panels of biomarkers, i.e., “haematology–lipid-related factor” (i.e., ferritin, haemoglobin, HDL-c, and triglycerides), “proinflammatory–prothrombotic-related factor” (i.e., platelets, neutrophils, and C-reactive protein), “LDL-c–vitamin-related factor” (i.e., vitamins D and B12, and LDL-c), and “age–glucometabolic-related factor” (i.e., age and HbA1c), in relation to higher cIMT in patients with AS. Among these four clusters, “age–glucometabolic-related factor” was an independent predictor of increased cIMT (p < 0.001). Conclusions: In addition to traditional cardiometabolic risk factors, WC and LDL-c, the disease activity score (BASDAI) is independently related to subclinical atherosclerosis in AS patients. The joint involvement of heterogeneous cardiometabolic risk factors may reflect different pathophysiological processes of subclinical atherosclerosis in patients with AS.