This study is intended to examine the motor skill learning and treadmill exercise on motor performance and synaptic plasticity in the cerebellar injured rats by harmaline. Experiment groups were divided into four groups and assigned 15 rats to each group. GroupⅠ was a normal control group(induced by saline); GroupⅡ was a experimental control group(cerebellar injured by harmaline); GroupⅢ was a group of motor skill learning after cerebellar injured by harmaline; GroupⅣ was a group of treadmill exercise after cerebellar injured by harmaline. In motor performance test, the outcome of groupⅡ was significantly lower than the groupⅢ, Ⅳ(especially groupⅢ)(p<.001). In histological finding, the experimental groups were destroy of dendrities and nucleus of cerebellar neurons. GroupⅢ, Ⅳ were decreased in degeneration of cerebellar neurons(especially groupⅢ). In immunohistochemistric response of synaptophysin in cerebellar cortex, experimental groups were decreased than groupⅠ. GroupⅢ's expression of synaptophysin was more increased than groupⅡ, Ⅳ. In electron microscopy finding, the experimental groups were degenerated of Purkinje cell. These result suggest that improved motor performance by motor skill learning after harmaline induced is associated with dynamically altered expression of synaptophysin in cerebellar cortex and that is related with synaptic plasticity.