This work presents a systematic study of the surface-enhanced Raman-scattering (SERS) properties of nanoparticle island substrates (NIS) and their application for oligonucleotide target detection. Using NIS that are structurally well characterized by atomic force microscopy (AFM) and UV-VIS extinction spectrum, it demonstrates the correlation of nanostructure of substrates and extinction maximum (λmax)of substrates fabricated on different conditions, i.e. thickness of metal Ag. To effectively implement SERS on NIS and find out optimal condition for DNA detection, the relationship between extinction maximum (λmax) and SERS enhancement factor (EF) was explored in detail. In fact, this work demonstrates high S/N ratio SERS spectra can be achieved for NIS with λmax within a spectrum window (~60nm) consisting by the excitation wavelength (514nm) and the scattered Raman wavelength, and highest EF measured is about out 4 ×108 with thickness of Ag being 50A. Detection of oligonucleotide target has been performed with a sandwich assay scheme. In this scheme a layer of thiol modified receptor oligonucleotide was assembled on NIS and 3' of oligonucleotide probe has been labeled with a Raman-active dye. Furthermore, We compared the detection performance of strategies using probe oligonucleotide with or without gold nanoparticles (Au-NPs,20nm) capped on 5'. The experimental results reveal that the DNA detection implemented with NIS can provide high sensitivity, and both dynamic range and diction limit can be amplified with the aid of Au-NPs on 5' of probes. The current detection limits of NIS with and without Au-NPs are 0.4 femtomolar and 1 nanomolar respectively.