Surface enhanced Raman spectroscopy (SERS) detection in microfluidics is an interesting topic for its high sensitivity, miniaturization and online detection. In this work, a SERS detection in microfluidics with the help of the Ag nanowire aggregating based on dielectrophoresis (DEP) is reported. The Raman intensities of molecule in microfluidics is greatly enhanced in the naturally generated nanogaps of Ag nanowire aggregating modulated by DEP. Firstly, the influence of DEP voltage and time on Ag nanowire aggregating is investigated to figure out the optimal condition for SERS. And then, the SERS intensities of methylene blue and rhodamine6G at various concentration with high reproducibility and uniformity are studied. Furthermore, the experiment data demonstrate this DEP-SERS system could be repeated used for different molecule detections. At last, the SERS of melamine is measured to explore its application on food safety. Our work anticipates this nanowire assisted repeatable DEP-SERS detection in microfluidics with high sensitivity could meet the emerging needs in environmental pollution monitoring, food safety evaluation, and so on.