<p>Advancements in construction material and technology have led to bridge structures with longer spans. The complex finite element models of long-span bridges significantly increase the computational demand and time required for nonlinear time history analysis. Additionally, conventional uniform excitation assumptions, which neglect the intricate spatial variation of earthquakes, are inappropriate for the dynamic analysis of long-span bridges. Against this backdrop, an efficient unconditionally stable explicit KR-α algorithm is employed for structural dynamic analysis and compared with the implicit Newmark algorithm. Meanwhile, the spatial variation of ground motion and soil-structure interaction effect are comprehensively investigated. Initially, a full-bridge finite element model of the Sutong Bridge is developed on the software platform of OpenSees. Subsequently, the structural dynamic analysis and fragility analysis under diverse seismic excitation patterns and constraint conditions are discussed. The results demonstrate that the KR-α algorithm can effectively save the computational time of the long-span bridge without compromising accuracy. Moreover, the maximum difference of damage probability for bridge system between uniform and non-uniform excitations could reach up to 14.7%. Thus, it is suggested to consider the spatial variation of ground motions for the seismic design and assessment of long-span bridges.</p>