Despite a few studies, our knowledge of functional connectivity in the basal ganglia-thalamo-cortical loop remains incomplete in Parkinson’s disease mouse model. Here, we investigated alterations of functional connectivity and white matter structure in a hemi-parkinsonian mouse model. We found that the fractional anisotropy significantly decreased in the lesioned side in the subthalamic nucleus, such as medio-dorsal nucleus and centromedian nucleus of thalamus. The functional connectivity in the ipsilateral thalamic nuclei was also decreased in hemiparkinsonian mice. These results indicate that ipsilateral thalamic nuclei are key regions for functional and structural alterations in basal ganglia-thalamo-cortical loop in hemiparkinsonian mice.