A temperature-controlled submillimeter-gap (500 μm) rheo-magnetic resonance imaging (MRI) Couette cell has been developed to measure confined flow of soft structured materials under controlled temperature. The proposed setup enables performing rheo-MRI measurements using (i) a spatially uniform temperature control over the range 15°C to 40°C and (ii) a high spatial resolution up to 10 μm, as a consequence of the improved mechanical stability of the in-house developed rotating elements. Here, we demonstrate the performance of the cell for the rheo-MRI velocimetry study of a thixotropic fat crystal dispersion, a complex fluid commonly used in food manufacturing. The submillimeter-gap geometry and variable temperature capability of the cell enable observing the effects of shear- and temperature-induced fat recrystallization on both wall slip and shear banding under strongly confined flow. Our improved rheo-MRI setup opens new perspectives for the fundamental study of strongly confined flow, cooperative effects, and the underlying interparticle interactions and for ultimately aiding optimization of products involved in spreading/extrusion, such as cosmetics and foods.