The evolution of the optical properties of GaN nanowires (NWs) with respect to a sequence of surface functionalization processes is reported; from pristine hydroxylated to finally, 3-mercaptopropyltrimethoxysilane (MPTMS) functionalized GaN NWs. Photoluminescence, Raman, stationary, and time-resolved photoluminescence measurements were applied to investigate the GaN NWs with different surface conditions. A documented surface passivation effect of the GaN NWs induced by the MPTMS functionalization is determined based on our characterization results. A hypothesis associated with the surface band bending and the defect levels near the band edges is proposed to explain the observed experimental results.