The invention discloses a semi-active shock absorption controlling device and method for a large aqueduct under longitudinal shock input. The method comprises the steps that a magneto-rheological damper is used as a controller; a spencer model of the magneto-rheological damper is used to simulate shock absorption; an LQR/LQG control law is used to design active control, and the optimal state feedback gain is obtained in an LQR method; the magneto-rheological damper is combined with an aqueduct structure so that the semi-active control device achieves an optimal active control force approximately, and a semi-active control law is designed; the space dynamic force of the aqueduct structure is calculated in a beam segment finite element method; and in the process of tentative calculation of the optimal control force, the form and size of weight matrixes Q and R are continuously adjusted to obtain the active control force through which control effect and force are comprehensively optimal. The device comprises an aqueduct body, a support, a basin type rubber bearer, a lead-core rubber bearer, a dilatation joint, the magneto-rheological damper and a pier top. The method and structure are simple, the dynamic scope is wide, the endurance is high, and the damping force can be continuously adjusted.