Mechanical deformation has been proposed to influence the proton conduction of perfluorosulfonic acid (PFSA) polymer membranes. We conducted a series of all-atom molecular dynamics simulations to understand how stretching affects the structural and dynamic properties of hydrated membranes composed of different equivalent weights (EWs) of PFSA at different water contents. The simulations reveal that the Young's modulus and yield stress of the membrane decreases with increasing water content, which is qualitatively in good agreement with experimental observations. When the PFSA membrane was stretched along a particular axis, the ionomer backbone chains became extended along the stretching direction and were aligned parallel to each other. The elongation of the ionomer backbone enhances hydronium ion diffusivity in the stretching direction at low water content. However, at high water content, the side chains orient themselves perpendicularly to the stretching direction in order to associate with free hydronium ions; this results in lower hydronium ion mobility. Furthermore, the higher EW PFSA is better aligned along the direction of stretching than the lower EW PFSA. The effect of stretching on proton transport is more pronounced in the higher EW PFSA membrane.