An ultrasensitive surface-enhanced Raman spectroscopy (SERS) aptamer sensor (aptasensor) using a noble metal nanoparticle-magnetic nanospheres composite was developed for L-theanine detection. It makes use of Fe3O4@Au MNPs and Au@Ag NPs embedded with the Raman reporter 4-mercaptobenzoic acid (4MBA). Au@4MBA@Ag NPs modified by aptamer and Fe3O4@Au MNPs modified by cDNA created the aptasensor with the strongest Raman signal of 4MBA through the specific binding of the aptamer. With the preferred binding of L-theanine aptamer to L-theanine, Au@4MBA@Ag NPs were released from Fe3O4@Au MNPs, causing a linear decrease in SERS intensity to achieve the SERS detection of the L-theanine. The SERS peak of 4MBA at 1078cm-1 was used for quantitative determination. SERS intensity showed a good log-linear relationship within the range 10-10 to 10-6Mof L-theanine. Theaptasensor has a high selectivityfor L-theanine compared with other twelve testedanalytes. Hence, thisaptasensor is a promising analytical tool for L-theanine detection. The developedmethod was appliedto the analysis of real samples, demonstrating excellent performance. The comparison with the standard liquid chromatography mass spectrometry methodshowed an error within 20%.