In this study, numerical simulations are employed to investigate the hydrodynamic performance and wake topology of a swimming Rhinoptera javanica. The study is motivated by the quest to understand the hydrodynamics of median and paired fin(MPF) mode with both spanwise and chordwise flexibility. The simulations employ an immersed boundary(IB)-simplified sphere function-based gas kinetic scheme(SGKS) method that allows us to simulate flows with complex moving boundaries on fixed Cartesian grids. A computational model is constructed based on biological data. The evolution of the hydrodynamic force and 3D vortex structures are presented. Besides, the effect of frequency and amplitude are also discussed to explain some behaviors of the actual Rhinoptera javanica. This work can provide a baseline for the design of a bio-inspired underwater vehicle. INDEX TERMS MPF, flexibility, swimming/flying, bio-inspired, biological fluid dynamics.