<p>Previous earthquakes indicate that near-source canyon topographic effect (NCTE) can substantially amplify the seismic responses of canyon-crossing bridges (CCBs). While the conventional practices are to make disaster response decisions based on the deterministic approaches, it cannot provide a holistic view regarding the impacts of uncertainties of ground motions on CCBs. Thus, this study adopts the performance-based assessment in a probabilistic framework to evaluate the seismic fragility of CCBs considering NCTE. For this purpose, a numerical model of a typical tall-pier CCB across a V-shaped canyon is constructed using the OpenSees. Eighteen ground motions combined with NCTE are simulated using the region-matching method. PGA, Sa(T1), and PGV are compared to determine the optimal intensity measure (IM). The probabilistic seismic demand models and fragility curves are constructed. The results show that PGV is the optimal IM for ground motions considering NCTE. The NCTE can significantly increase the damage probability of CCBs. The damage probability of the side bearing is the most sensitive to NCTE among the vulnerable components. The side pier bearings and the side piers on the illuminated canyon side are the most vulnerable components in cases with and without consideration of NCTE, respectively.</p>