Alfv en eigenmodes (AEs) destabilized by the neutral beam injection (NBI) in a Large Helical Device experiment are investigated using multi-phase magnetohydrodynamic (MHD) hybrid simulation, which is a combination of classical and MHD hybrid simulations for fast ions. The fast ion distribution is simulated with NBI, collisions, and losses in the equilibrium magnetic field in the classical simulation, while the MHD hybrid simulation takes account of the interaction between fast ions and an MHD fluid, in addition to the classical dynamics. It is found in the multi-phase hybrid simulation that the stored fast ion energy is saturated due to the interaction with AEs at a lower level than that of the classical simulation. Two groups of AEs with frequencies close to those observed in the experiment are destabilized alternately at each hybrid simulation. Firstly destabilized are two toroidal Alfv en eigenmodes whose frequency is close to the local minimum of the upper Alfv en continuous spectrum. Secondly destabilized is a global Alfv en eigenmode whose frequency is located well inside the Alfv en continuous spectrum gap. In addition, two AEs whose frequencies are close to that of the ellipticity-induced Alfv en eigenmode are observed with a lower amplitude. When the hybrid simulation is run continuously, the interchange mode grows more slowly than the AEs, but becomes dominant in the long time scale. The interchange mode oscillates with a constant amplitude and a frequency of $1 kHz. The interchange mode reduces the stored fast ion energy to a lower level than that of the AEs.