We proposed a facile method to prepare the nitrogen-doped graphene quantum dots (NGQDs) doped silica (NGQDs@SiO2) nanoparticles (NPs). The NGQDs@SiO2 NPs were further explored as a versatile signal indicator for ochratoxin A (OTA) aptasensing by combination with electrochemiluminescence (ECL) and fluorescence (FL) detection. In this strategy, the core-shell Fe3O4@Au magnetic beads (MBs) acted as a nanocarrier to immobilize the thiolated aptamer specific for OTA, and the amino modified capture DNA (cDNA) was efficiently tagged with NGQDs@SiO2 NPs. The multifunctional aptasensor was thus fabricated by assembly of the NGQDs@SiO2 NPs onto the surface of Fe3O4@Au MBs through the high specific DNA hybridization between aptamer and cDNA. Upon OTA incubation, the aptamer linked with Fe3O4@Au MBs preferred to form an aptamer-OTA complex, which resulted in the partial release of the preloaded NGQDs@SiO2 NPs. The more OTA molecules in the detection system, the more NGQDs@SiO2 NPs were released into the bulk solution and the less preloaded NGQDs@SiO2 NPs were accumulated on the magnetic electrode surface. This provided a dual channel for OTA detection by combination with the enriched solid-state ECL and homogeneous FL detection. The FL assay exhibits a wide dynamic range and is more reproducible due to the homogeneous detection while the ECL assay possesses a lower detection limit and is preferable by using a cheaper instrument. One can obtain a preliminary screen from FL assay and a more accurate result from ECL assay. Integrating the virtues of dual analytical modality, this aptasensing strategy well-balanced the rapidity, sensitivity, and dynamic range, making it promising to other targets with aptamer sequences.