The invention discloses a shock absorption control method of an aqueduct structure under the action of random loads. The method includes the steps that r controllers are added onto an n-freedom-degree structure, and a semi-active control system motion equation of the structure under input of random loads is established; a virtual stimulation method is adopted for simulating the random loads to introduce a state vector, and a state equation of the structure is determined; a performance objective function of a system is defined, a minimum value of the performance objective function is used, and feedback gain can be obtained; semi-active control is performed on virtual response through a magnetorheological damper, and therefore random shock of the aqueduct structure can be effectively controlled. According to the method, the semi-active control method is adopted for calculating the aqueduct structure under the action of the random loads, and random features of actual stimulation are represented with the virtual stimulation method; the method is simple and convenient to operate and solves the problem that the semi-automatic control system is influenced because output variables are disturbed randomly.