Stroke recovery with changes in volume and perfusion of grey matter (GM) tissues remains largely unknown. We hypothesized that GM atrophy co-existed with GM plasticity presenting with increased volume and perfusion in specific regions in the period of post-stroke recovery. Twelve well-recovered stroke patients with pure subcortical lesions in the middle cerebral artery-perfused zone were included. All of them underwent structural and perfusion magnetic resonance imaging (MRI) examinations at admission and a mean of 6 months after stroke onset. Differences in GM volume (GMV) on structural images and cerebral blood flow (CBF) derived from perfusion images between two examinations were compared using voxel-based morphometry. The associations between changes in GMV and CBF with clinical scores were analysed. Decreased GMV was found in post-central gyrus, pre-central gyrus, precuneus, angular gyrus, insula, thalamus and cerebellum, and increased GMV was found in hippocampus, orbital gyrus and lingual gyrus (all corrected P < 0.05) at the follow-up examination. Increased CBF was found in subcallosal cingulate gyrus, hippocampus and lingual gyrus (all corrected P < 0.05) at the follow-up examination. Only decreased GMV in the anterior lobe of cerebellum was negatively associated with improvement of Barthel index (β = -0.683, P = 0.014). Our study provides the imaging evidence of GM atrophy co-existing with GM plasticity involving in increased volume and perfusion in specific regions (including cognition, vision and emotion) in well-recovered stroke patients, which advances our understanding of neurobiology of stroke recovery.