An aptamer-antibody sandwich electrochemical immunosensor was studied. Fe3O4/MWCNTs-COOH/Nafion was modified and fixed on a glassy carbon electrode to amplify electrical signals. The antibody was coupled with AuNPs to form conjugates. It captures the target free thyroxine (FT4) and forms antibody-AuNPs/FT4 macromolecular complexes. The complex is then captured by the aptamer on the glassy carbon electrode and detected by the electrochemical workstation using differential pulse voltammetry (DPV). Under the best conditions, the prepared sensor showed a linear relationship in the concentration range 0.1 to 105 pg/mL and the detection limit (LOD) was 0.04 pg/mL. The sensor can enhance the adsorption capacity of target FT4 and detect FT4 stably and with high selectivity. The aptamers and antibodies are free from additional modifications. In addition, the high recovery of the proposed sensor was verified by testing the human serum samples. The immunosensor has the advantages of simple operation, rapid recognition process, and short response time. These results indicate that the immunosensor is expected to achieve rapid and effective detection of FT4 in early pregnancy and evaluate thyroid function in the future. The research ideas of this work will also be applicable to the detection of other small molecules and provide ideas for the detection of other substances.