Surface-enhanced Raman scattering (SERS) has been emerged as one of the most promising strategies in chemical and biomolecular detection due to high sensitivity and label-free identification in binding kinetics and cost of metal pattern preparation. In this study, I fabricate microspheres with hierarchical surface nanopatterns using microfluidic device for molecular detection based on surface-enhanced Raman scattering. Briefly, a photocurable silica-ETPTA suspension was emulsified into monodisperse droplets using a microfluidic device composed of two coaxial glass capillaries. The silica particles in each droplet protruded through the interface and spontaneously formed a hexagonal array. After photopolymerization of the droplets, I selectively decorated the exposed areas of the silica particles with silver nanoparticles through silver mirror reaction. The resulting hierarchically structured microspheres showed high sensitivity and fast binding kinetics in molecular detection based on SERS, owing to the dense array of hot spots on each microsphere and high mobility of the microspheres, respectively. Notably, the SERS signals from molecules adsorbed on the microspheres could be detected in both the dried and suspension states. In addition, I demonstrate that the SERS-active microspheres can be functionalized into structural colored or magnetoresponsive microspheres for advanced applications.