Objective To study the regional cerebral blood flow (rCBF) in important brain functional areas and the metabolic levels of these brain functional areas in patients with primary hypothyroidism by using arterial spin labeling (ASL) and magnetic resonance spectroscopy (MRS) techniques to explain the possible causes of brain dysfunction in patients with primary hypothyroidism. Methods Twenty-five patients with primary hypothyroidism (newly diagnosed and not treated) who were treated in the endocrinology department of our hospital were selected as the research group, and 25 healthy patients with normal thyroid function who came to our hospital during the same period with matched gender and age were selected as the control group. ASL and MRS techniques were used to detect and calculate regional cerebral blood flow (rCBF) in the frontal lobe, hippocampus, and posterior cingulate gyrus, as well as N-acetylaspartate/creatine (NAA/Cr), choline/creatine (Cho) in the brain/Cr, and inositol/creatine (mI/Cr) ratio. The correlations between metabolite ratios measured by rCBF, MRS, and serum TSH, FT3, and FT4 levels were analyzed. Results Compared with the control group, the rCBF in the frontal lobe, hippocampus, and posterior cingulate gyrus of the dominant hemisphere of the hypothyroid patients in the study group decreased significantly (P < 0.05). The comparison of metabolite ratios showed that compared with the control group, the NAA/Cr ratio of the frontal lobe and posterior cingulate gyrus of the study group was significantly decreased, and the Cho/Cr ratio of the posterior cingulate gyrus of the study group was significantly increased. The MI/Cr ratio of the hippocampus was significantly decreased (all P values < 0.05). Correlation analysis showed that rCBF and NAA/Cr in posterior cingulate gyrus were significantly negatively correlated with serum TSH levels (P < 0.05). Conclusion The changes of rCBF and metabolite ratios in the frontal lobe, hippocampus, and posterior cingulate gyrus of patients with primary hypothyroidism can be detected using ASL and MRS techniques. The changes of rCBF and metabolite ratio and their negative correlation with serum TSH level are helpful to explain the causes of brain dysfunction in patients with primary hypothyroidism.