Performance improvement of advanced polymer electrolyte membranes requires control over the morphology as it plays an important role for mechanical, thermal, and proton transport properties. The ionic domain orientation of films cast from sulfonated block copolymer solutions is generally anisotropic, and to maximize proton conductivity in fuel cell applications, hydrophilic channel alignment is desirable. In this work, a series of multiblock copolymers based on sulfonated copolyimides were synthesized and characterized by NMR, TEM and AFM microscopy, and impedance spectroscopy. For constant ion exchange capacity, the higher the block length, the higher the proton conductivity and water uptake for a given relative humidity. A random copolymer exhibited the lowest performance, in particular at low relative humidity, caused by a reduced phase separation as derived from AFM and TEM measurements. Orientational order probed by H-2 NMR on absorbed D2O showed preferential alignment in the through-plane direction. However, proton pulsed-field-gradient (PFG) NMR along the two orthogonal membrane directions revealed water diffusion to be faster in-plane than in the through-plane direction. This difference in diffusion is attributed to a lamella-like structure composed of rather short, through-plane hydrophilic channels in our systems. For the block copolyimide with the highest block length, two distinct diffusion processes could be identified. This is ascribed to a superimposed morphology on the micrometer scale, leading to an opaque appearance of the membrane.