Ultrasensitive Surface Plasmon Resonance (SPR) detection of small molecules can be achieved using nanoparticles to both enhance the SPR signals and pre-concentrate low levels of target analytes in the sample. However, the short effective penetration depth of the SPR evanescent field, and steric hindrance of binding when immobilizing small molecules on surfaces, limits the applicability of using relatively large nanoparticles (≥100 nm) for SPR detection. To overcome the issues of steric hindrance, this paper investigates the role of the molecular linkers to tether both the antibodies to the magnetic nanoparticles, and to bind the small molecules to the surface of the SPR chips. By extending the distance of the small molecule (progesterone) away from the SPR chip surface and improving the antibody orientation on the large magnetic nanoparticles, a sensitive SPR detection for progesterone was achieved in buffer (0.013 ng mL-1). The results of the SPR assay for progesterone in milk were in good correlation with ELISA results, and could be used to verify the onset of estrus in cows.