A surface‐enhanced Raman spectroscopy (SERS) detection method that allows dynamic on‐demand generation of SERS substrates at locations of interest for in situ molecular sensing is demonstrated. Thermal convection and thermophoresis, which are both generated in a laser‐induced temperature gradient, are used to accumulate suspended plasmonic nanostructures to form 3D SERS substrate. Raman signals of melamine, which is used as a model analyte, increase to ≈117‐fold within 2 min of laser irradiation because of the accumulation. In addition, it is demonstrated that the accumulation of the nanostructures is reversible, and that reproducible SERS effects can be obtained during a repeated heating and cooling process. Because of the capability of on‐demand generation of a high density of SERS hot spots at different locations in solution, this particle manipulation and SERS detection method is applicable to monitor temporal and spatial variations of the concentrations of molecules. The complexity of the detection system remains the same when using this method since all the measurements are performed with a conventional Raman system and simple fluid channels. The required temperature gradient is generated by the laser used to excite Raman signals, and no nanofabricated substrates and complicated microfluidic or optical components are needed.