In this paper, a simple method to fabricate a three-dimensional (3D) nanostructure decorated with Ag nanoparticles for surface-enhanced Raman scattering (SERS) is demonstrated. Highly ordered porous anodic aluminum oxide (AAO) templates were employed to construct these compound nanostructures. First, the AAO templates were fabricated using a two-step anodization approach. Second, an alternating current (AC) electrochemical deposition was used to fill AAO templates with Ag nanoparticles. Taking 4-mercaptopyridine (4-MPy) as the probing molecule, high-quality SERS spectra were observed. The UV-vis mirror reflection spectra were measured to investigate the surface plasma resonance (SPR) absorbance. An interesting phenomenon of SPR-affected thin film interference was observed. SERS mapping was performed to characterize the homogeneity of as-prepared substrates. Good homogeneity and stability make these substrates good candidates for SERS spectroscopy.