Lateral ankle sprains (LAS) might lead to joint sensory deafferentation, which induces maladaptive neuroplasticity, especially the morphological atrophy of the cerebellar vermis. However, longitudinal evidence on the causality of injury and neural differences is still lacking. To this end, this study aimed to determine whether the morphology of the central nervous system would be altered before and after ligament transection in LAS mouse models. A total of 40 C57BL/6 mice were randomly divided among the LAS, Sham and Blank groups. We repeatedly performed the balance beam test and neural voxel-based morphometry (VBM) measurements using an 11.7 T magnetic resonance imaging before and 2 months after the surgery. The results showed that for balance outcomes, the LAS group had a significantly longer time and more slips of the balance beam tests compared with the Sham and Blank groups at 2 months after surgery, with no significant difference among the three groups before surgery. Regarding the VBM analysis, the LAS group showed significantly lower VBM values in the central lobule III of the cerebellar vermis and medial amygdalar nucleus (MEA) compared with the Sham and Blank groups after surgery, with no significant difference among the three groups before surgery. In conclusion, lateral ligament injuries might lead to morphological atrophy of the cerebellar vermis in animal models, which might pave the way for the pathological process of ankle instability after LAS.