Surface-enhanced Raman scattering (SERS) can enhance Raman signals through adsorbing target molecules on the surface of metal nanostructures with strong electromagnetic fields. However, it is difficult to deposit target molecules without complicated pre-treatment steps. In this research, we introduce SERS-active microgels containing highly-concentrated gold nanoparticles. Water-in-oil-in-water double emulsion drops were prepared by counter-flow-microfluidics. The core of the drops contain gold nanoparticles and hydrogel precursors. As imposing positive osmotic pressure on the drops, the water in the core flows out and the concentration of gold nanoparticles increased by a factor of 30-40. Finally, the highly-concentrated gold nanoparticles are trapped through gelation of the core under UV. The microgel system of SERS substrates worked as a molecular sieve and it provided molecular selectivity. Well-distributed gold nanoparticles with high concentration provide signal enhancement and reproducibility.