Achieving an equilibrium between the self-healing performance and thermo-mechanical properties of polymers is crucial, but exploration of the properties of self-healing polymers based on dynamic covalent bonding (DCB) in microphaseseparated polymer structures remains underinvestigated. This study examines the effects of microphase separation on the self-healing and thermo-mechanical properties of a poly(dimethylsiloxane), bis(3-aminopropyl) terminated, herein denoted as PDMS, crosslinked acrylic copolymer with hindered urea bonds (HUB). This combination leverages the benefits of both acrylic copolymers and PDMS. The phase separation of the self-healing copolymer was manipulated by using solvent blending and thermal annealing methods. Two PDMSs with different molecular lengths were used to study the effects on domain size and cross-linking density. It was confirmed that solvent blending curtails microphase separation, leading to crushed nanodomains of PDMS, while thermal annealing promotes clear microphase separation with distinct nanodomains. The observations from microphase morphology, stress− strain curves, moduli, and hardness indicate a significant correlation between self-healing performance, mechanical properties, and microphase-separated structure. The self-healing capabilities of this material were validated at nano (nanoscratch test via AFM), micro (single-scratch test using optical microscopy), and macro (crosscut-healing test using UTM) scales. These findings highlight the material's versatile nanostructures and mechanical properties, achieved through different processes, and its potential applicability in a wide range of fields.