To investigate the value of proton magnetic resonance spectroscopy (1H-MRS) on the diagnosis of SCA3/MJD, and to calculate the correlation between 1H-MRS ratio and the clinical score. Methods: Sixteen patients with SCA3/MJD and 19 healthy volunteers were scanned with 1H-MRS. The data of N-acetyl aspartate, creatine, choline-containing compounds, myoinositol, NAA/Cr, Cho/Cr, and mI/Cr ratio were collected, which were grouped for comparative study. The onset patients with SCA3/MJD were evaluated with the International Cooperative Ataxia Rating Scale and Scale for the Assessment and Rating of Ataxia, the correlation between NAA/Cr, Cho/Cr or mI/Cr ratio and the clinical score was calculated. Results: The NAA/Cr in the pons and cerebellar dentate nucleus from the onset patients with SCA3/MJD was significantly reduced compared to that in the normal control group. The NAA/Cr in the cerebellar dentate nucleus of onset patients with SCA3/MJD was obviously correlated with ICARS. Conclusion: SCA3/MJD lesions are mainly located in the cerebellum and brainstem, where gray and white mater are also involved. The cerebellar dentate nucleus may be the earliest involved area. There is a correlation between the ICARS and the cerebellar lesion degree. The ICARS reflects the severity of clinical manifestations. 1H-MRS is useful in the diagnosis of SCA3/MJD.