In this study, we demonstrate the synthesis and application of magnetic plasmonic gyro-nanodisks (GNDs) for Fourier transform surface plasmon resonance based biodetection. Plasmonically active and magnetically responsive gyro-nanodisks were synthesized using electrochemical methods with anodized aluminum templates. Due to the unique properties of GNDs (magnetic responsiveness and surface plasmon bands), periodic extinction signals were generated under an external rotating magnetic field, which is, in turn, converted into frequency domains using Fourier transformation. After the binding of a target on GNDs, an increase in the shear force causes a shift in the frequency domain, which allows us to investigate biodetection for HA1 (the influenza virus). Most importantly, by modulating the number and the location of plasmonic nanodisks (a method for controlling the hydrodynamic forces by rationally designing the nanomaterial architecture), we achieved enhanced biodetection sensitivity. We expect that our results will contribute to improved sensing module performance, as well as a better understanding of dynamic nanoparticle systems, by harnessing the perturbed periodic fluctuation of surface plasmon bands under the modulated magnetic field.