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Abstract Studies have shown that the co-occurrence of diabetes mellitus (DM) and thyroid dysfunction (TD) exacerbates diabetes complications and imposes a financial burden on the healthcare system. Therefore, this study aimed to investigate the prevalence of TD-DM comorbidity and its associated risk factors. This cross-sectional study was conducted on enrollment phase data of the TABARI cohort population which consisted of 10,255 adults aged between 35 to 70 years old residing in Sari, Mazandaran, Iran from 2015 to 2017. A total of 9939 out of 10,255 individuals (96.92%) entered the study. The prevalence of TD among T2DM patients was 13.2%. The prevalence of T2DM among patients with TD was 9.2%. Furthermore, the prevalence of TD-DM comorbidity in the overall population was 2.2%. Logistic regression analysis revealed that the odds of TD-DM comorbidity was significantly higher in women (OR 2.85; 95% CI 1.58–5.11), in the age group of 60–70 years (OR 9.62; 95% CI 3.69–25.10), in smokers (OR 2.32; 95% CI 1.19–4.52), in individuals with high waist circumference (WC) (OR 2.22; 95% CI 1.32–3.75), in individuals with low high-density lipoprotein (HDL) (OR 1.60; 95% CI 1.20–2.14), in individuals with high total cholesterol (TC) (OR 1.71; 95% CI 1.21–2.41), in individuals with high triglycerides (TG) (OR 1.79; 95% CI 1.27–2.51), and significantly lower in individuals with higher physical activity (PA) (OR 0.67; 95% CI 0.49–0.93). The present study demonstrated a prevalence of 2.2% in patients with both TD and T2DM. Additionally, female gender, older age, smoking, high WC, low HDL, high TC, high TG, and low PA were predictors of TD-DM comorbidity.