The surface treatment of chopped glass fiber (GF) can significantly improve the strength, impact resistance, and durability of epoxy resin (EP), and the homogeneity of GF modified EP material is better than that of continuous fiber reinforced EP, which has an important application in the engineering field. The effects of surface treatment and addition of chopped GF on the rheological behavior and mechanical properties of EP/modified chopped GF composites were studied by alcohol washing, coupling agent treatment, and acid etching modification methods. In addition, a reactive flame retardant containing phosphorus, nitrogen and bromine was synthesized, and the flame retardant application was studied in the EP/modified chopped GF system. The results show that the surface micromorphology of the chopped GF treated with acid etching is relatively rough, which can greatly increase the initial shear viscosity of the system, and the mechanical properties of the cured composites are significantly better than those of the GF treated with alcohol treatment and coupling agent. The chopped GF content of acid etching treatment is 2.0%, and the tensile strength of the composite is the highest, which is 59.75 MPa. When the flame retardant content is 10%, the peak heat release rate and total heat release of the composite are significantly lower than those of pure EP, and the mechanical properties are improved at the same time.