The surface enhanced Raman spectroscopy (SERS) has been employed in the structural characterization successfully due to its ultra-high sensitivity. However, it is still remained the significant difficulties in the precise interpretation of spectroscopy. Thus, it was not developed as the promising tool for monitoring the organic reaction directly. Herein, by using the two dimensional Au nanoparticles array film as substrate, the SERS was hyphenated with high performance liquid chromatography (HPLC). The individual advantages of high sensitivity of SERS and high efficiency in separation of HPLC were combined together, and it was extended successfully to real-time monitor of a Suzuki coupling reaction between 3-bromopyridine and phenylboronic acid. Firstly, the retention time and SERS spectra of standard solution of 3-bromopyridine and phenylboronic acid were performed respectively. It was beneficial for distinguishing the reactants of the current Suzuki reaction. After the reaction was proceeded for about 5 minutes, the mixture was sampled for the HPLC-SERS detection. It demonstrated that the chromatogram peaks located at 2.1 min and 2.8 min were contributed to phenylboronic acid and 3-bromopyridine, while 3.6 min and 15.3 min were originated from the reaction products. The solution collected at different retention times were then flowed through the catheter and dropped to the surface of Au nanoparticles arrays sequentially. The SERS spectra features were well agreement with that of 3-bromopyridine at 2.8 min, while the SERS spectra was absent for phenylboronic acid at 2.1 min due to its weak adsorption on Au surface. For the products, the typical vibrational modes of 3-phenylpyridine and diphenyl were observed in the SERS spectra, suggesting the composition of the product and byproduct. Meanwhile, the final product was confirmed by NMR spectroscopy, proving a structure of 3-phenylpyridine. Finally, the SERS results were well associated with the chromatographic peaks in a certain duration. It indicated that the HPLC-SERS technique would be a promising tool as a complementary approach to traditional techniques (such as LC-MS) for on line monitoring the organic reaction processes.