The hydronium ion catalyzed vinyl alcohol-acetaldehyde isomerization was investigated via ab initio molecular orbital (MO) calculations with/without a dielectric continuum (DC) method and Monte Carlo (MC) simulations with the statistical perturbation theory. The cluster models, composed of CH2=CHOH, H3O+, and H2O molecules, were considered, and the potential energy profiles of double proton transfers both in the gas phase and in the aqueous solution were obtained by nb initio MO calculations. In order to clarify the mechanism suitable for the reaction, two possible mechanisms, concerted and stepwise, have been proposed. Our results indicated that the double-proton transfers prefer to occur separately not only in the gas phase but also in the aqueous solution, to support the preference for the stepwise mechanism. The solvent effect difference between the DC method and MC simulations was also examined along the stepwise reaction path by plotting the free energy profiles. It was found that MC simulations improve considerably the energy barrier of activation by the DC method (5.0 kcal/mol) to present 13.5 kcal/mol for the free energy barrier of activation. The present value shows good accordance with the experimental value, i.e., 15.2 kcal/mol.