Here, we proposed a surface-enhanced Raman scattering (SERS) pump-free microfluidic chip (LoC-SERS) based on a D-amino acid oxidase (D-AAO)-mediated cascade reaction to accomplish rapid quantitative analysis of D-proline (D-Pro) and D-alanine (D-Ala) associated with gastric cancer (GC). Novel Sesame seed globular Fe3O4@Au magnetic nanoparticles (SAuMNPs) modified with boronic acid probe 3-mercaptophenylboronic acid (3-MPBA) were first prepared as SERS nanolabels. Then, D-AAO selectively catalyzed D-Pro (or D-Ala) to generate H2O2 oxidized borates, with a new Raman peak at 882 cm−1. Based on this, a ratiometric analytical method was established for the quantitative analysis of D-Pro (or D-Ala). Utilizing a magnet-loaded pump-free LoC-SERS device as the detection platform, the magnetic SERS nanolabels passed through the reaction zone, and aggregated under the action of the miniature magnets, generating abundant “hot spots” for signal enhancement. Employing this strategy, D-Pro and D-Ala in saliva could be rapidly and accurately quantified with the limit of detection (LOD) down to the μM level. Moreover, with capillary drive technology, the analysis process was automatically integrated, eliminating the need for manual cleaning and heavy syringe pumps, making it highly simple and portable. A satisfactory specificity, stability, and reproducibility were achieved with this LoC-SERS device. Finally, the favorable results of saliva testing in GC patients suggested that this LoC-SERS strategy, combining the advantages of the highly specific enzymatic reaction and magnetic aggregation signal amplification, could provide a promising alternative tool for the dynamic monitoring of D-AAs.