The Negros–Sulu megathrust poses an imminent threat to coastal communities surrounding the Sulu Sea, but with limited information on past tsunamis, megathrust geometry, and locked segments, robust seismic and tsunami hazard assessments are hindered. To identify highly exposed coastal areas amid this knowledge gap, we estimated the Negros–Sulu megathrust source parameters using a structural-based segmentation and scaling-relation approach for tsunami modeling. A total of 18 sets of source parameters from six segments and three dip angle scenarios were considered with moment magnitude and average slip of Mw 8.0–8.9 and 1.68–6.23 m, respectively. Tsunami simulations were modeled in JAGURS, accounting for nonlinear shallow water equations, horizontal and vertical seafloor displacements, and Boussinesq dispersion effects. Coastal regions directly facing the segments have the highest exposures with <2 min arrival times, highlighting the major control of wave directivity and the need for rapid evacuation strategies. The Negros Trench generates up to 6 m wave height and 7 m/s flow velocity, while the Sulu Trench up to 8 m and 6 m/s. Coastal areas with ≥2 m wave heights typically exhibit a concave morphology with a nearshore width interquartile range of 2–4.5 km. At wider nearshore width (>20 km), wave dissipation results in lower wave heights (<2 m) that underscore accurate nearshore bathymetry in tsunami modeling. This study provides exposure maps of the maximum wave height, flow velocity, and minimum arrival times from rupture scenarios for searching paleotsunami deposits and most importantly for policymakers, local government, and coastal communities to mitigate tsunami hazard risk.