The thermoresponsive behavior of two molecular brushes having poly(propylene oxide)-poly(ethylene oxide) copolymer side chains is investigated in aqueous solution, where the side chains have longer contour lengths than the backbone. The brushes differ in the side-chain architecture; they are either a diblock (PbE) or a random copolymer (PrE). For both types of brushes, an overall rodlike shape at room temperature is revealed by cryo-electron microscopy. A polymer-rich central part and a water-rich outer part are identified by small-angle neutron scattering (SANS). Upon heating up to the cloud point, the shell of PbE weakly dehydrates, while the one of PrE severely dehydrates along with a cylinder-to-disk transformation. Moreover, the aggregates formed above the cloud points feature significantly different inner structures: PbE aggregates are composed of strongly interpenetrating brushes, while PrE aggregates consist of loosely packed brushes. These differences indicate the important role of the side-chain architecture in the thermal dehydration behavior and the associated structural changes.