This article investigates the efficiency of a new generation smart isolation system, namely shape memory alloy wire-based lead rubber bearing, for the seismic response control of long-span cable-stayed bridge systems under near-fault ground motions. The constitutive model of shape memory alloy wire-based lead rubber bearings is coded and implemented into OpenSees as a new user element. This user element can accurately predict the re-centering capability and energy dissipation capacity of shape memory alloy wire-based lead rubber bearing under different excitations. The Sutong cable-stayed bridge in China, with a main span of 1088 m, is taken as an example. Results reveal that implementing shape memory alloy wires into lead rubber bearings can effectively increase the self-centering property and, as a result, reduce the residual deformation in shape memory alloy wire-based lead rubber bearings under near-fault ground motions. Shape memory alloy wires lead to an increase in the horizontal stiffness and energy dissipation capacity of shape memory alloy wire-based lead rubber bearings. The deck displacement is restricted effectively, and a superior structural performance is achieved in terms of the deck acceleration. Shape memory alloy wire-based lead rubber bearings can effectively reduce the base shear and base moment of the towers. However, it is observed that an increase in the shape memory alloy wire diameter may have negligible effect on the deck acceleration, tower base shear and moment, and in some cases, on the pier base shear and moment.