Methyl rotation induced by proton transfer was found for cis-N-methylacetamide (NMA). More interestingly, it was found that the microenvironment could control the methyl rotation. The atom-centered density matrix propagation (ADMP) method, a recently developed ab initio molecular dynamics, was further carried out to depict the trajectories for methyl rotation of NMA. Moreover, trajectories for methyl rotation of NMA complexed with water molecules were also calculated, and water molecules at the two different sites of NMA were found to reverse or cease the rotational direction of the methyl groups of NMA. This finding that microenvironment can not only control rotational direction of methyl groups but can also cease the rotation may be of significant importance for the control of molecular machines.