A new strategy to toughen epoxy resins through control of topological structure of cross-linking network has been presented. With a tertiary amine initiator, the curing proceeded via chain-wise polymerization. The impact strength of epoxy resin increased to above 84 kJ/m2 by only increasing the curing temperature, which is much higher than the reported value of 10–30 kJ/m2 for pure epoxy resin. Meanwhile, yielding was found during uniaxial tensile and three-point bending measurements. At the molecular scale, the cross-linking density showed a bimodal distribution and decreased with increasing curing temperature. A mechanism based on controlled topology of cross-linking network has been proposed to explain these changes. The cross-linking of epoxy resins occurs via a continuous anionic ring-opening polymerization, resulting in well interpenetrated chains. The chain transfer converts active alkoxide anions into inactive hydroxyls, limiting the linear growth and cross-linking. The resultant branching structures display lower cross-linking density, serving as native tougheners at the segment scale. Chain transfer accelerates with temperature, thus the ductility increases monotonically with curing temperature. This mechanism was confirmed by deliberately introducing branching chains through a short time of high-temperature reaction at the first stage of curing. The impact strength was enhanced by 2.5 times in comparison to the samples without the initial high-temperature curing. This unique and facile strategy shows potential in directly obtaining more ductile epoxy resins materials by controlling the topology of cross-linked networks.