The multiphoton ionization of pyrimidine-(water)(n) clusters at conditions of supersonic expansion is studied using a time-of-flight mass spectrometer at the wavelengths of 355 and 532 nm. At both wavelengths, a series of protonated C4H4N2-(H2O)(n)H+ cluster ions are obtained. The production of these protonated cluster ions requires an intracluster proton transfer reaction. The protonated products are also suggested to relate to the excitation or ionization of water molecules. Ab initio calculations show that the dissociation of C4H4N2-(H2O)(n)(+) cluster ions prefer to produce protonated ions. Two ways of producing protonated cluster ions are discussed. The reaction mechanism of intracluster proton transfer and the geometric structures of pyrimidine-(water)(n) clusters were depicted. The proton pulling effect and the atomic charge changes in the protonated cluster ions are also discussed.