Hyperbranched epoxy resins with a silicone skeleton (HERSS) obtained by us through an environmentally-friendly synthetic method have shown a prominent comprehensive performance in modifying the diglycidyl ether of bisphenol-A (DGEBA). However, controlling the performance of the HERSS is still a challenge. In this paper, we report the preparation of three other kinds of HERSS with various molecular weights via hydrosilylation, in order to study the effect of the molecular weights of the HERSS on the degree of branching (DB), the viscosity and the mechanical performance, the thermal properties and the micro-phase separation behavior of cured HERSS–DGEBA composites, which contain the HERSS prepared recently. The degree of branching and viscosities of the HERSS are 0.71–0.84 and 103.5–697.4 mPa s, respectively. An increase in the molecular weight of the HERSS results in a decrease in the DB and an appearance of a maximum viscosity. Accordingly, the mechanical properties of the cured HERSS–DGEBA composites, including the tensile, flexural and impact strength, increase first and then decrease, and their glass transition temperatures decrease weakly. Both the average diameters of 3.62–4.75 μm and the distribution of the islands in the “sea–island” structure of all the cured composites show an increase. Compared with those of DGEBA, the tensile, flexural and impact strength could be increased by about 76.4–88.6%, 25.3–36.0% and 78.4–92.1%, respectively, but their glass transition temperature was impaired only by about 6.3–6.8%.