Temporomandibular joint disorders (TMDs) are closely related to the masticatory muscles, but objective and quantitative methods to evaluate muscle are lacking. IDEAL-IQ, a type of chemical shift-encoded magnetic resonance imaging (CSE-MRI), can quantify the fat fraction (FF). The purpose of this study was to develop an MR IDEAL-IQ-based method for quantitative muscle diagnosis in TMD patients. A total of 65 patients who underwent 3 T MRI scans, including CSE-MRI sequences, were retrospectively included. MRI diagnoses and clinical data were reviewed. There were 19 patients in the normal group and 46 patients in the TMD group with unilateral disc displacement. The TMD group was subdivided into those with and without clenching. The right and left FF values of the masseter, medial, and lateral pterygoid muscles were measured twice by two oral radiologists on CSE-MRI, and the average value was used. FF measurements using CSE-MRI showed excellent intra- and inter-observer agreement (ICC > 0.889 for both). There were no statistically significant differences between the right and left FF values in the masseter, medial pterygoid, and lateral pterygoid of the normal group (p > 0.05). A statistically significant difference was found in the TMD group without clenching, in which the masseter muscle had a statistically significantly lower FF value on the disc displacement side (3.94 ± 1.61) than on the normal side (4.52 ± 2.24) (p < 0.05). CSE-MRI, which can reproducibly quantify muscle FF values, is expected to be a biomarker for objective muscle evaluation in TMD patients. The masseter muscle is expected to be particularly useful compared to other masticatory muscles, but further research is needed.