Metallic plasmonic nanoparticles generate surface-enhanced Raman Scattering (SERS) for wide sensing applications of biomolecules, gas and environmental contaminants. However, the metallic materials cause high thermal radiation during laser excitation in the opto-microfluidic systems and give rise to temporal intensity fluctuations, which is called blinking effects in SERS spectra. This work developed nanocomposite consisting of graphene oxide (GO) and gold nanoparticles (AuNPs) with high thermal stability and low thermal radiation, which provided plasmonic resonance while reduced blinking effect for SERS-based sensing in the microfluidic detection system. The system was applied to detect kanamycin in drinking water, orange juice, and milk by using Texas Red-dye conjugated Beacon aptamer, where the aptamer was designed to be specific and switchable in kanamycin recognition. The sensor was reusable, and its limit of detection was 0.75 nM in a linear range of 1 nM to 100 nM. The microfluidic SERS detection system can be potentially used for sensitive and reliable assays of small molecules.