We propose a molecular dynamics (MD) method based on the multi-component molecular orbital (MC_MO) method, which takes into account the quantum effect of proton directly, for the detailed analyses of proton transfer in hydrogen bonding system. The MC_MO based MD (MC_MO-MD) method is applied to the basic structures, H5O2+ (called “Zundel ion”), and its isotopomers (D5O2+andT5O2+). We clearly demonstrate the geometrical difference of hydrogen bonded O⋯O distance induced by H/D/T isotope effect because the O⋯O in H-compound was longer than that in D- or T-compound. We also find the strong relation between stretching vibration of O⋯O and the distribution of hydrogen bonded protonic wavefunction because the protonic wavefunction tends to delocalize when the O⋯O distance becomes short during the dynamics. Our proposed MC_MO-MD simulation is expected as a powerful tool to analyze the proton dynamics in hydrogen bonding systems.