Herein we report a simple, one-pot, surfactant-free synthesis of 3D Ag microspheres (AgMSs) in aqueous phase at room temperature. The 3D AgMSs act as supports to fix the gold nanoparticles (GNPs) in 3D space via the interaction between the carboxyl groups of GNPs and the Ag atoms of AgMSs. The ensemble of AgMSs@GNPs with high surface-enhanced Raman scattering (SERS) activity and sensitivity can be an ideal 3D substrate choice for practical SERS detection applications. The simple self-assembly strategy may be extended to other metallic materials with great potentials in SERS, catalysis, and photoelectronic devices.