Three-dimensional (3D) modeling of tsunami events is intended to promote tsunami safety. However, the developed 3D modeling methods based on Computational Fluid Dynamics and photorealistic particle visualization have some weaknesses, such as not being similar to the original environment, not measuring the wave’s end point, and low image accuracy. The method for 3D modeling of tsunamis that results from this research can fulfil those weaknesses because it has advantages, such as being able to predict the end point of waves, similar to the original environment, and the height and area of inundation. In addition, the method produces more detailed and sharper spatial data. Modeling in this research is conducted using Agisoft Metashape Professional software to a produce 3D orthomosaic from pictures taken with Unmanned Aerial Vehicle (UAV) technique or drone (photogrammetry), and 3ds max software is used for wave simulation. We take a sample of an area in Cilacap, Indonesia that was impacted by the 2006 southwest coast tsunamis and may be vulnerable to future big megathrust earthquakes and tsunamis. The results could be used to provide several benefits, such as the creation of evacuation routes and the determination of appropriate locations for building shelters.