Crosslinking thermosets with hyperbranched polymers confers them superior comprehensive performance. However, it still remains a further understanding of polymer crosslinking from the molecular chains to the role of aggregates. In this study, three hyperbranched polysiloxane structures (HBPSi-R) are synthesized as model macromolecules, each featuring distinct terminal groups (R denotes amino, epoxy, and vinyl groups) while similar molecular backbone (Si-O-C). These structures were subsequently copolymerized with epoxy monomers to construct interpenetrating HBPSi-R/epoxy/anhydride co-polymer systems. The spatial molecular configuration and flexible Si-O-C branches of HBPSi-R endow them with remarkable reinforcement and toughening effects. Notably, an optimum impact strength of 28.9 kJ mol-1 is achieved with a mere 3% loading of HBPSi-V, nearly three times that of the native epoxy (12.9 kJ mol-1). By contrasting the terminal effects, the aggregation states and crosslinking modes were proposed, thus clarifying the supramolecular-dominant aggregation mechanism and covalent-dominant dispersion mechanism, which influences the resulting material properties. This work underscores the significance of aggregate science in comprehending polymer crosslinking and provides theoretical insights for tailoring material properties at a refined molecular level in the field of polymer science.