MRI imaging with Neuromelanin contrast has been thrived in recent years. We adopted this method again to explore the LC contrast differences in multiple system atrophy (MSA). Three methods for quantifying LC contrast were used, which all had the ability to reproduce the results that LC contrast decreases in MSA. We further did subgroup analyses of MSA with orthostatic hypotension (MSA-OH) and MSA without orthostatic hypotension (MSA-nonOH). Interestingly, although LC contrast of the two subgroups were not significantly different, adverse correlations between LC contrast and autonomic dysfunction severity were found in MSA-OH and MSA-nonOH subgroups.