A three-dimensional smoothed-particle hydrodynamics (SPH) method is used to study the moving boundary problem of a swimming manta ray, focusing on Eulerian and Lagrangian coherent structures. The manta ray's boundary motion is predefined by a specific equation. The calculated hydrodynamic results and Eulerian coherent structures are compared with data from the literature. To improve computational stability and efficiency, the δ+-SPH model used in this study incorporates tensile instability control and an improved adaptive particle-refinement technique. By comparing and analyzing the Eulerian and Lagrangian coherent structures, the relationship between these vortex structures and hydrodynamic force generation is examined, revealing the jet mechanism in the manta ray's wake. The SPH method presented herein is robust and efficient for calculating biomimetic propulsion problems involving moving boundaries with large deformations, and it can accurately identify vortex structures. The approach of this study provides an effective simulation tool for investigating biomimetic propulsion problems such as bird flight and fish swimming.