Background: Cardiovascular disease (CVD) is the leading cause of morbidity and mortality in patients with type 2 diabetes (T2DM). Carotid intima-media thickness (CIMT) is considered a preclinical stage of atherosclerosis. Therefore, it is necessary to identify the related risk factors for CIMT to facilitate the early prevention of CVD. Previous studies have shown that visceral fat area (VFA) is a risk factor for T2DM and CVD. However, few studies have focused on the effects of VFA on CIMT associated with T2DM. Moreover, considering that the body fat distribution shows regional and racial heterogeneity, the purpose of this study was to investigate the predictive value of VFA and other risk factors for CIMT associated with T2DM in Western China. Methods: In a cross-sectional study, a total of 1372 patients with T2DM were divided into the CIMT (−) group (n = 965) and the CIMT (+) group (n = 407) based on CIMT values. In addition to the univariate analyses, logistic regression analysis and a decision tree model were simultaneously performed to establish a correlation factor model for CIMT. Results: Univariate analyses showed that sex, smoking status, age, heart rate, systolic blood pressure (SBP), diastolic blood pressure (DBP), height, weight, body mass index (BMI), waist circumference, hip circumference, waist-hip ratio, VFA, subcutaneous fat area, and the levels of 2-h C-peptide, serum creatinine, urea nitrogen and uric acid were significantly different between the two groups (all p < 0.05). Smoking, increased VFA, female sex and increased BMI were risk factors in the logistic regression analyses (OR = 5.759, OR = 1.364, OR = 2.239, OR = 1.186, respectively). In the decision tree model, smoking was the root node, followed by sex, waist circumference, VFA and chronic kidney disease (CKD) in order of importance. Conclusions: In addition to smoking, sex and BMI, VFA has a significant effect on CIMT associated with T2DM in the Chinese Han population in Western China. In addition, the decision tree model could help clinicians make more effective decisions, with its simplicity and intuitiveness, making it worth promoting in future medical research.