Silicon nanowire arrays (SiNWAs) decorated with metallic nanoparticle heterostructures feature promising applications in surface-enhanced Raman scattering (SERS). However, the densely arranged SiNWAs are usually inconvenient for the following decoration of metallic nanoparticles, and only the top area of silicon nanowires (SiNWs) contributes to the SERS detection. To improve the utilization of the heterostructure, herein, oblique SiNWAs were grown separately, and Ag nanoparticles (AgNPs) were uniformly deposited by magnetron sputtering to get the three-dimensional (3D) SiNWAs decorated with AgNPs (AgNPs-SiNWAs) SERS substrate. The large open surfaces of oblique SiNWs would create more surface area available for the formation of hotspots and improve the adsorption and excitation of analyte molecules on the wire. The optimized AgNPs-SiNWAs substrate exhibits high sensitivity in detecting chemical molecule Rhodamine 6G, and the detection limit can reach 1 x 10(-10) M. More importantly, the substrate also can be used as an effective DNA sensor for label-free DNA detection.