The "fixed" or "flexible" design of plasmonic hotspots is a frontier area of research in the field of surface-enhanced Raman scattering (SERS). Most reported SERS hotspots have been shown to exist in zero-dimensional point-like, one-dimensional linear, or two-dimensional planar geometries. Here, we demonstrate a novel three-dimensional (3D) hotspot matrix that can hold hotspots between every two adjacent particles in 3D space, simply achieved by evaporating a droplet of citrate-Ag sols on a fluorosilylated silicon wafer. In situ synchrotron-radiation small-angle X-ray scattering (SR-SAXS), combined with dark-field microscopy and in situ micro-UV, was employed to explore the evolution of the 3D geometry and plasmonic properties of Ag nanoparticles in a single droplet. In such a droplet, there is a distinct 3D geometry with minimal polydispersity of particle size and maximal uniformity of interparticle distance, significantly different from the dry state. According to theoretical simulations, the liquid adhesive force promotes a closely packed assembly of particles, and the interparticle distance is not fixed but can be balanced in a small range by the interplay of the van der Waals attraction and electrostatic repulsion experienced by a particle. The "trapping well" for immobilizing particles in 3D space can result in a large number of hotspots in a 3D geometry. Both theoretical and experimental results demonstrate that the 3D hotspots are predictable and time-ordered in the absence of any sample manipulation. Use of the matrix not only produces giant Raman enhancement at least 2 orders of magnitude larger than that of dried substrates, but also provides the structural basis for trapping molecules. Even a single molecule of resonant dye can generate a large SERS signal. With a portable Raman spectrometer, the detection capability is also greatly improved for various analytes with different natures, including pesticides and drugs. This 3D hotspot matrix overcomes the long-standing limitations of SERS for the ultrasensitive characterization of various substrates and analytes and promises to transform SERS into a practical analytical technique.