Surface-enhanced Raman scattering (SERS) spectroscopy as a powerful tool has been used to explore different catalysis degradation reactions, whereas some drawbacks caused by ferric ions still exist in the current SERS monitoring of the Fenton reaction process. In this work, microfluidic droplet- and alginate microparticle-based methods were, respectively, applied to realize SERS monitoring of the Fenton degradation process in a relatively stable environment, which benefited from reduction of the loss of ferrous ions and the aggregation of the SERS substrate. As expected, the spectroscopic evidence at the molecular level directly revealed the degradation mechanism of rhodamine dyes, showing that the chemical bonds between xanthene and carboxybenzene broke continuously during the reaction. Afterward, the degradation mechanism determined by SERS was verified via mass spectrometry detection, which confirmed the validity of the SERS-based method. More broadly, the microfluidic droplet- and microparticle-based methods are potentially applicable for SERS monitoring of more Fenton degradation reactions.