Rationale and objectives <p>This study aims to investigate the feasibility of using modified Dixon Quantification sequence (m-DIXON Quant) to quantitatively assess thyroid fat fraction (FF) and compare the differences between healthy volunteers and patients with hypothyroidism (HT), so as to evaluate its application value in differential diagnosis.</p> Materials and methods <p>Between January 2023 and December 2023, routine thyroid MRI examinations were performed on 92 volunteers and 52 patients with hypothyroidism (HT), and thyroid fat content was assessed using the m-Dixon Quant. Independent sample t-tests were used to compare differences in age, gender, BMI, and FF between healthy volunteers and HT patients. Receiver operating characteristic (ROC) curve analysis was conducted to evaluate the discriminative ability of FF in distinguishing HT patients from healthy volunteers.</p> Results <p>The thyroid FF of HT patients (<i>n</i> = 52) (67.15 ± 14.68) was significantly higher than that of healthy volunteers (30.20% ± 8.91%), with statistically significant difference (<i>P</i> = 0.000). FF was significantly negatively correlated with thyroid hormone levels (FT4: <i>r</i> = − 0.810; FT3: <i>r</i> = − 0.628;) and significantly positively correlated with thyroid-stimulating hormone (TSH) (<i>r</i> = 0.884). Thyroid FF demonstrated excellent diagnostic efficacy in distinguishing HT patients from healthy volunteers, with a receiver operating characteristic curve area (AUC) of 0.910, sensitivity of 0.928, and specificity of 1.000.</p> Conclusion <p>This study demonstrated that the increase in thyroid FF was primarily associated with the hypothyroid state itself, rather than being solely driven by differences in age, gender, or adiposity. m-DIXON Quant had great potential in distinguishing patients with hypothyroidism from healthy volunteers, which was of great significance for evaluating the treatment effect of hypothyroidism patients.</p>