In this study, we investigated the effect of the arrangement of Ag nanodomes on the performance of a plasmonic refractive index sensor. As a template of Ag nanodomes, polystyrene (PS) bead layers with surface coverages of 56 and 90% and a multilayered structure were created. The optical properties and sensing performance of Ag nanodomes were characterized by reflection spectroscopy and bulk refractive index sensing. The Ag nanodomes created on the closely packed and multilayered PS beads exhibited similar reflection spectra and bulk refractive index sensitivity. The differences between these Ag nanodomes were in the resonance wavelength and the corresponding reflective colors. By reducing the surface coverage of PS beads, the reflectance decreased, the resonance dip appeared at a longer wavelength, and the bulk refractive index sensitivity was improved to 516 nm per refractive index unit (RIU). The experimental results revealed that the arrangement of Ag nanodomes has a notable influence on their optical properties and needs to be optimized to improve the performance of plasmonic biosensors.