In this work, the three most stable uracil isomers (U 1, U2, and U3) and their neutral, positive, and negative charged multihydrates are chosen as research objects to investigate the tautomeric process between the most stable uracil, U1, and its two minor stable isomers, U2 and U3. By the study, deeper insight can be obtained regarding point mutations induced by uracil deformation. Toward the target, the activation energies of the intramolecular proton transfer (tautomeric process) as well as the catalysis effects of water molecules and of charges attached are investigated using density functional theory (DFT) calculations by means of the B3LYP exchange and correlation functions. Results reveal that water molecules hold a stronger catalysis effect on the proton transfer in these negative charged uracil hydrates than in the neutral counterparts. The optimal number of water molecules needed to catalyze the proton transfer is determined as two in the neutral hydrated systems, whereas it is three in the negative charged systems. Positive charge attachment, however, hinders the intramolecualr proton transfer of uracil, and the charge and the proton Of Uracil will transfer to the water clusters if water molecules are attached. Then the positive charged hydrates look more like U1 a/b+[(H2O)(n)+H+] species in structure. Analysis reveals that it is the acceptance process of the last proton to determine the impossibility of proton transfer and result in the failure of tautomeric processes from cat-U1a-nw to cat-U2-nw and from cat-U1b-nw to cat-U3-nw. Detailed structural parameters and energy changes are discussed for the above different processes.