Size-dependent Raman spectra of the hexagonal (β)-phase Yb3+,Er3+ codoped NaYF4 nanophosphors and dynamic probing of the upconversion luminescence (UCL) are reported. Raman scattering results show the normal red shifts of Raman peaks but anomalous line narrowing with decreasing the particle sizes. The phonon confinement effects are believed to be dominated by the surface vibrational energies in affecting UCL. Dynamic decay data are then applied to quantitatively verify the surface effects and size-dependent UCL. Dynamic probing is shown to be an efficient tool to both qualitatively and quantitatively characterize the upconversion nanophorphors (UCNPs) that have no “quantum efficiency.” The findings are relevant to the engineering of the nanostructures of the UCNPs for the applications of the bioimaging and photodynamic therapy.