Thermally rearrangeable aromatic polyamides (TEMPO-PA) and random copolyamides (TEMPO-PA-COON) incorporating alkoxyamine moieties in the main chain were synthesized, and the effects of thermal reorganization behavior on their solution and solid-state structures were investigated. The hydrodynamic radius in solution decreased as the solution temperature increased because of the dissociation of the alkoxyamine unit. Additionally, the dry density of the thin films decreased as the fabrication temperature increased because of the suppression of polymer aggregation caused by the thermally induced radical crossover reaction. In addition, at the film surface of the random copolyamide containing hydrophobic TEMPO and hydrophilic 3,5-diaminobenzoic acid (DABA) units, the hydrophilicity decreased as the fabrication temperature increased. This is because hydrophobic TEMPO and hydrophilic DABA units tend to be discretely aggregated near the film surface to minimize the surface energy and suppress the hydrogen bonding via a radical crossover reaction during the thin-film fabrication process. The present study clearly shows that both the solution structure and the solid-state molecular aggregation structure of the dynamic covalent polymers can be easily controlled by a thermal trigger, and it provides a new method for controlling the higher-order structure of polymer solutions and solids.