The thickness and roughness of metal layers substantially affect the performance of surface plasmon resonance (SPR)-based sensors. The deposition methods, control parameters, and substrate characteristics influence the layer thickness and roughness. This study investigates the SPR characteristics of a polished optical fiber surface coated with gold (Au) metal of different thicknesses. The Au layer is deposited via the thermal evaporation method, and its thickness is varied by controlling the deposition time (3–6 minutes). A proportionality relationship between thickness and deposition time is observed. Island-shaped structures in gold (Au) morphology are formed due to low adhesion to the substrate. The shape of this island creates gaps in the layer, causing scattering. In addition, the roughness on the gold surface triggers the Localized Surface Plasmon Resonance (LSPR) phenomenon. As a result, the measured dielectric characteristics differ from the reference. The SPR curve calculation simulation was carried out based on reference optical parameters and measurement results by an ellipsometer, which were then compared with experiments. The obtained results show that the substrate roughness, morphology, and thickness of the Au layer play an essential role in determining the characteristics of the SPR curve in a fiber optic plasmonic sensor. As a result, in basic experiments, the sample with an Au thickness of 27.37 nm (deposition time = 3 min) shows better characteristics (half-maximum full width, minimum transmittance, and resonance wavelength) compared with the sample with an Au thickness of 53.97 nm (deposition time = 4 min), Although 53.97 nm is the optimal thickness from the simulation using reference optical parameters (smooth substrate surface and smooth gold layer).