In the Large Helical Device (LHD) experiments using fast protons and fast deuterons, hybrid simulations were performed with the MEGA code to investigate the synergistic effects of multiple fast-ion species on instabilities and fast-ion transport, where multiple fast ions interact with the magnetohydrodynamic fluid. In the MEGA simulations, the burst amplitude of Alfvén eigenmodes (AEs) after the fast-ion stored energy reaches a steady state is larger than that before the steady state, leading to a significant increase in the fast-ion loss rate. The dominant AE frequencies obtained in the simulations are in good agreement with those observed in the experiments. In the case of multiple fast-ion species, additional AEs appear that are absent when only a single fast-ion species drives the AEs, and these modes are caused by the redistribution of multiple fast ions. Consequently, these additional AEs lead to increased loss rates of both fast protons and fast deuterons. The synergistic effect of multiple fast-ion species is thus shown to enhance fast-ion transport and losses in the LHD.