The present invention provides a modified bismaleimide prepolymer, a resin composition and application thereof. The modified bismaleimide prepolymer is obtained by a reaction of a bismaleimide compound with an amino organosilicone resin A and an amino organosilicone resin B, where the amino equivalent (Ea.sub.A) of the amino organosilicone resin A is different from the amino equivalent (Ea.sub.B) of the amino organosilicone resin B, and the ratio of the total mass of the amino organosilicone resin A and the amino organosilicone resin B to the mass of the bismaleimide compound is (5-80):100. According to the present invention, the reactivity of the bismaleimide compound is improved, and the rheological property of the modified bismaleimide prepolymer applied in the field of substrate materials such as packaging substrates during lamination at high temperature is controlled.