The deformation of hydrated Nafion 117 was implemented using full-atomistic molecular dynamics simulation method to elucidate how the mechanical deformation affects the structure and transport of hydrated Nafion membrane. First, Nafion 117 membrane was equilibrated with 20 wt. % water content through an annealing procedure. The simulated characteristic correlation length and the diffusion coefficient of water and hydronium ions were analyzed for comparison with those observed in experiments. Then, the equilibrated Nafion membrane was deformed uniaxially up to 300 % of strain with a constant strain rate. The change in nanophase-segregation of hydrated Nafion during the deformation process was characterized using a directional structure factor as well as the pair correlation function in order to achieve fundamental understanding of the relationship of such structural change as a function of strain with the proton transport. It was found from the pair correlation analysis that the sulfonate distribution and sulfonate-hydronium correlation became stronger through the deformation while the hydronium ion solvation and the internal structure of water phase were not dependent on the deformation. From the directional structure factor profile, it was found that the long range correlation was developed in the perpendicular direction to the extension. The diffusions of water and hydronium ions were enhanced by 30 and 2 %, respectively, after the deformation. From this study, we suggested that it is desirable to investigate the proton transport using simulation methods covering larger dimensions with a long time scale.