A fluorescent aptasensor was developed and applied to detect aflatoxin B1 based on Au@Fe3O4/aptamers/aminofunctioned carbon quantum dots magnetic nanocomposites which were constructed self-assembly. The selective interactions between aflatoxin B1 and the aptamer in the samples cause release of the aminofunctioned carbon quantum dots which remains in the solution after magnetic separation. A linear fluorescence signal response to aflatoxin B1 concentration is obtained over a wide aflatoxin B1 concentration range of 0.001~1.00 ng/mL with a detection limit of 0.3 pg/mL, and the correlation coefficient is 0.996 4. The performances of the fluorescent sensor are significantly improved as the background fluorescence is effectively removed by magnetic separation.