An electrochemiluminescence (ECL) sensor based on Ru(bpy)₃²⁺-doped silica nanoparticles (RuSi NPs) combined with molecularly imprinted polymer (MIP) has been developed for the determination of ochratoxin A (OTA). The sensor was fabricated by remodification of RuSi NPs with a thin film of molecularly imprinted polymer, which provided the specific binding sites for OTA. The process of template elution and rebinding acted as a gate to control the flux of probes, which passed through the cavities and reacted with Ru(bpy)₃²⁺ immobilized on the electrode surface to emit ECL signal. The ECL intensity decreased with the OTA molecules rebound in MIP. The as-prepared sensor exhibited a very high sensitivity and excellent selectivity to the target molecule. The ΔI_ECL depended linearly on the logarithm of the OTA concentration in the range from 0.1 pg/mL to 14.76 ng/mL with lower detection limit of 0.027 pg/mL (S/N = 3). The MIP-ECL sensor enabled the successful application of this method to determine OTA in corn.