A sensitive luminescent bioassay for the detection of ochratoxin A (OTA), a small molecular mycotoxin, was developed using aptamer-conjugated magnetic nanoparticles (MNPs) as the recognition and concentration element and upconversion nanoparticles (UCNPs) as highly sensitive labels. The bioassay system was fabricated by immobilizing aptamer DNA 1 sequence onto the surface of Fe(3)O(4) MNPs, which were implemented to capture and concentrate OTA from bulk samples. The aptamer DNA 1 sequence then hybridized with UCNPs modified with DNA 2 sequence, which could dissociate from DNA 1 and result in a decreased luminescent signal when aptamer DNA 1 recognized and bound to target OTA. Under the optimal conditions, the decreased luminescent intensity (ΔI) is proportional to the concentration of OTA in the range of 1 × 10(-13) to 1 × 10(-9) g mL(-1) with a detection limit of 1 × 10(-13) g mL(-1). The proposed method then was successfully applied to measure OTA in naturally contaminated maize samples and validated by a commercially available enzyme-linked immunosorbent assay (ELISA) method. Benefiting from the magnetic separation and concentration effect of MNPs, the high sensitivity of UCNPs, as well as the selectivity and stability of the aptamer, the present upconversion luminescent bioassay offers a promising approach for the screening of small molecular mycotoxins because it is simple, rapid, highly sensitive, specific, does not require sample pre-concentration and lacks interference from autofluorescence of other biomolecules.