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This paper develops an improved three-dimensional sphere discontinuous deformation analysis (SDDA) model and uses UAV-based photogrammetry to enable SDDA to numerically analyze potential long-runout debris flows in Zheduotang area along the Sichuan-Tibet railway. First, the original SDDA is improved by proposing a sphere-sphere bonding algorithm to bond spheres with tetrahedral layout to form four-sphere clusters to approximate non-sphere particles in debris flow. Second, the capacity of the improved SDDA is verified by comparing modelling results with four groups of laboratory tests of granular flow. Third, UAV-based photogrammetry is used to obtain the real morphology of the extremely complex terrain surface of Zheduotang area which is finally transferred into a large number of triangular faces as the fixed boundary faces of SDDA. Then, three potential debris flow scenarios on this terrain surface are numerically studied, and some suggestions for engineering disaster prevention are drawn. Model performance shows that, the improved SDDA is a feasible tool to simulate debris flows. With the help of UAV-based photogrammetry, it shows significantly helpful for geohazard prevention for infrastructures in mountainous areas like the Sichuan-Tibet railway. • An improved sphere discontinuous deformation analysis model is proposed. • The validation of the improved model in debris flow simulation is verified. • UAV-based photogrammetry to parameterize the extremely complex terrain surface of mountainous area is used. • Engineering-scale long-runout debris flow simulations are carried out. [ABSTRACT FROM AUTHOR]