We report here a facile approach for flexible integration of high efficiency surface enhanced Raman scattering (SERS) monitors in a continuous microfluidic channel. In our work, femtosecond laser direct writing was adopted for highly localizable and controllable fabrication of the SERS monitor through a multi-photon absorption (MPA) induced photoreduction of silver salt solution. The silver substrate could be shaped into designed patterns, and could be precisely located at the desired position of the microchannel bed, giving the feasibility for real-time detection during reactions. SEM and TEM images show that the silver substrates were composed of crystallized silver nanoplates with an average thickness of 50 nm. AFM results reveal that the substrates were about 600 nm in height and the surface was very rough. As representative tests for SERS detection, p-aminothiophenol (p-ATP) and flavin adenine dinucleotide (FAD) were chosen as probing molecules for microfluidic analysis at visible light (514.5 nm) excitation, exhibiting an enhancement factor of ~10(8). In addition, the combination of the SERS substrate with the microfluidic channel allows detection of inactive analytes through in situ microfluidic reactions.