Surface Enhanced Raman Spectroscopy (SERS) has been developed as one of powerful tools for monitoring the organic reaction due to its extremely high sensitivity. Moreover, SERS provided the abundant fingerprint spectroscopic information for the structure analysis, and it could be integrated with other techniques to achieve the on-line detection. Microfluidic technology, due to its significant role in the miniaturization, integration and portability of instrument, exhibits the promising application in biomedicine, high throughput drug screening, the environment monitoring and protection. In recent years, the microfluidic chip as one of the modern technology for analyzing various substances at the same time has been rapidly developed. Compared with the conventional technique, it has the significant advantage and convenience, such as low reagent consumption, short reaction time, high reaction efficiency and so on. Herein, the microfluidic chip was employed as the microreactor for organic reaction with the ultralow dosage, and the SERS detection was integrated into the microreactor to realize the continuous monitoring on the substrates and products. The magnetic core-shell nanoparticles Fe3O4@Ag acted as the SERS substrate with reasonable magnetism and SERS activities, and it demonstrated that the magnetic nanoparticles was flowed in the microchannel of microfluidic chip and was enriched by the external magnetic field. The introduction of magnetic nanoparticles is beneficial to improve the detection sensitivity by the magnetic aggregation and to reach the continuous SERS detection by applying and retracting external magnetic field. At the same time, it exhibited the significant advantages of low amount of reactants, high efficiency and easy to realize on-line detection and high throughput screening in organic synthesis. The micro-synthesis of α-phenylethanol and the real-time monitoring of SERS are performed by the alternative enrichment and de-enrichment of magnetic nanoparticles in the present case. By changing the flow rate of reactants in the channel of microfluidic chip, different concentrations of reactants and products were obtained in a certain duration. The influence of the spectral features from the reactants was eliminated by differential spectrum technique, and the distinctive SERS spectrum of α-phenylethanol was presented accordingly. It demonstrated that the integration of microfluidic chip and SERS technique could be developed as a powerful tool for on-line monitoring organic reactions and exhibits the promising application in high throughput screening of organic chemical reactions.