The epoxy resin was mixed with ammonium polyphosphate (APP) and hyperbranched silicon-containing polymers (HBP-B2). The cured composites were investigated by thermogravimetric analysis, Underwriters Laboratory standard for the flammability properties under vertical burning (UL-94V), and limited oxygen index (LOI) test methods. The LOI of 43.5 and could be obtained at the weight ratio of 70:25:5 for the epoxy resin:APP:HBP-B2, Sample A25B5, and the LOI was higher than that of the composite with 30 wt % APP only, Sample A30B0, of which the LOI was 34.5. It suggested that the HBP-B2 could cooperate with the epoxy/APP composite to form a more effective protection layer during combustion, which resulted in a higher second-stage thermal degradation temperature. During the UL-94V test, the flame was extinguished immediately once the burner was removed. Furthermore, the tensile and impact strength of the epoxy/APP composite could also be improved by using HBP-B2 compound as the toughening agent. The composite containing 20% of APP and 10% of HBP-B2, Sample A20B10, still had excellent flame retardant properties with a V-0 rating. Moreover, the tensile strength and impact strength of that composite got 19 and 25% increases compared with the Sample A30B0, which contained 30% of APP only.