The phenomenon of hydraulic jump is an exciting and complex hydraulic problem, and it is widely used in practice to dissipate the energy of irrigation-hydroelectric projects. With a hydraulic jump on the rough bottom, through experiments, many characteristics of hydraulic jump have been studied, such as depth after jump y2 and jump length Lj. However, understanding the evolution of vortex structure in rough bottom hydraulic jump presents a significant challenge to experiment and theory. The formation, development, and breaking of the vortex structure at the foot of the hydraulic jump and the rough bottom area have been analyzed and elucidated. This study simulated a hydraulic jump on the rough bottom using the Flow-3D hydraulic model. With the obtained results, the authors have used several vortex identification methods to clarify the evolution of vortex structure in the rough bottom hydraulic jump. Compared with the Q criterion, the Liutex/Rortex method is more effective in detecting vortexes. The results provide a further understanding of the phenomenon of hydraulic jumps.