Tinnitus involves the perception of sound in the absence of external acoustic stimuli. The underlying mechanisms of tinnitus have been investigated using noninvasive, whole brain functional imaging methods. However, the changes in the subcortical auditory system are less well understood. To address this knowledge gap, we conduct an auditory fMRI on a well-established sodium salicylate-induced rodent tinnitus and hyperacusis model. The results reveal frequency-dependent changes in auditory subcortical structures, inferior colliculus and lateral lemniscus by salicylate induced tinnitus. This study has advanced our understanding of subcortical auditory processing during tinnitus/hyperacusis and advances the rat model for further fMRI investigations.