Protonated water cluster is one of the most important hydrogen-bond network systems. Finding an appropriate DFT method to study the properties of protonated water clusters can substantially improve the economy in computational resources without sacrificing the accuracy compared to high-level methods. Using high-level MP2 and CCSD(T) methods as well as experimental results as benchmark, we systematically examined the effect of seven exchange-correlation GGA functionals (with BLYP, B3LYP, X3LYP, PBE0, PBE1W, M05-2X, and B97-D parametrizations) in describing the geometric parameters, interaction energies, dipole moments, and vibrational properties of protonated water clusters H+(H2O)2-9,12. The overall performance of all these functionals is acceptable, and each of them has its advantage in certain aspects. X3LYP is the best to describe the interaction energies, and PBE0 and M05-2X are also recommended to investigate interaction energies. PBE0 gives the best anharmonic frequencies, followed by PBE1W, B97-D and BLYP methods. PBE1W, B3LYP, B97-D, and X3LYP can yield better geometries. The capability of B97-D to distinguish the relative energies between isomers is the best among all the seven methods, followed by M05-2X and PBE0. [ABSTRACT FROM AUTHOR]