Self‐assembled materials such as lyotropic liquid crystals offer a wide variety of structures and applications by tuning the composition. Understanding materials behavior under flow and the induced alignment is wanted in order to tailor structure related properties. A method to visualize the structure and anisotropy of ordered systems in situ under dynamic conditions is presented where flow‐induced nanostructural alignment in microfluidic channels is observed by scanning small angle X‐ray scattering in hexagonal and lamellar self‐assembled phases. In the hexagonal phase, the material in regions with high extensional flow exhibits orientation perpendicular to the flow and is oriented in the flow direction only in regions with a high enough shear rate. For the lamellar phase, a flow‐induced morphological transition occurs from aligned lamellae toward multilamellar vesicles. However, the vesicles do not withstand the mechanical forces and break in extended lamellae in regions with high shear rates. This evolution of nanostructure with different shear rates can be correlated with a shear thinning viscosity curve with different slopes. The results demonstrate new fundamental knowledge about the structuring of liquid crystals under flow. The methodology widens the quantitative investigation of complex structures and identifies important mechanisms of reorientation and structural changes.
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