The invention relates to hyperbranched silicon-phosphorus synergistic flame retardant modified epoxy resin and a preparation method thereof. The resin is composed of an epoxy phosphorus-containing hyperbranched polysiloxane flame retardant, bisphenol-A epoxy resin, an anhydride-type curing agent and a tertiary amine-type curing accelerator. On the one hand, a synergistic flame retardant of a hyperbranched structure contains both silicon and phosphorus flame retardant elements, and the synergistic effect between different flame retardant elements achieves an excellent flame retardant effect. Onthe other hand, the hyperbranched phosphorus-silicon synergistic flame retardant contains a large number of epoxy groups which can participate in a curing reaction together with epoxy resin and has good compatibility with a resin matrix, wherein a large number of nano-scale cavities reduce the crosslinking density of a resin system; and at the same time, Si-O-Si soft segments are introduced intothe epoxy resin, thereby effectively improving the toughness of the resin system. Various functional groups can be introduced to an active end through formulation, so that the epoxy resin can be endowed with different properties, and the hyperbranched silicon-phosphorus synergistic flame retardant modified epoxy resin has broad application prospects in aerospace, electronic packaging and other fields.