Sensitive in situ detection of organic molecules is highly demanded in environmental monitoring. In this work, the surface enhanced Raman spectroscopy (SERS) is adopted in microfluidics to detect the organic molecules with high accuracy and high sensitivity. Here the SERS substrate in microchannel consists of Ag nanoparticles synthesized by chemical reduction. The data indicates the fabrication conditions have great influence on the sizes and distributions of Ag nanoparticles, which play an important role on the SERS enhancement. This result is further confirmed by the simulation of electromagnetic field distributions based on finite difference time domain (FDTD) method. Furthermore, the SERS spectra of organic molecule (methylene blue) obtained in this plasmonic microfluidic system exhibit good reproducibility with high sensitivity. By a combination of SERS and microfluidics, our work not only explores the research field of plasmonics but also has broad application prospects in environmental monitoring.