The invention discloses a generalized predictive control-containing comprehensive energy system scheduling method and system. The method comprises the steps of modeling an energy conversion device andan energy storage device in a comprehensive energy system respectively, and obtaining an energy supply model of the energy conversion device and an energy supply model of the energy storage device; constructing an energy conversion device controller according to the generalized predictive control; determining a target function, and solving the energy supply model of the energy conversion device and the energy supply model of the energy storage device according to the target function to obtain a predicted output value of the energy conversion device and the capacity of the energy storage device; setting the scheduling duration, and correcting and controlling the predicted output value of the energy supply model of the energy conversion device through an energy conversion device controllerand according to the device constraint conditions and the capacity of the energy storage device, thereby realizing the energy scheduling, realizing the accurate control of the comprehensive energy system, and improving the problems that a traditional energy scheduling method is worse in scheduling flexibility and accuracy.