The present study was undertaken to investigate the effects of physical practice on excitability changes in human primary motor cortex (M1) during motor imagery (MI). Using different intensities of transcranial magnetic stimulation (TMS), we examined changes in the motor evoked potential (MEP) of the first dorsal interosseous (FDI) muscle with and without MI, and before and after physical practice. On comparing results for MEPs recorded before and after physical practice, the difference between the MEP amplitudes observed at rest and during MI only increased at higher TMS intensities. This finding indicates a physical practice-dependent increase of the higher threshold recruitment of corticospinal tract neurons (CTNs), consistent with synchronization for efficient movement, and provides evidence that neural mechanisms of MI depend not only on the type of movement but also on the extent of the motor adaptation (the physical practice). These present findings also show the benefit of MI and highlight beneficial neural mechanisms related to the activation of M1 during MI. In other words, MI may reflect functional changes of M1 that are similar to the changes observed after physical practice.