Recently, bisphenol AF (BPAF) as most commonly used bisphenol A analogs had the increasing higher level in the environment with unknown risks. Herein, a synchronous dual-mode sensor had been established based on differential pulse voltammetry (DPV) and electrochemiluminescence (ECL) for the detection of BPAF in pond mud. Firstly, the sensing molecularly imprinted polymer (MIP) films were prepared by electrochemical polymerization procedure with 3,4-ethoxylene dioxy thiophene (EDOT) as the functional monomer, BPAF as the template molecule and MXene as the supporting electrolyte. Due to unique characters of PEDOT and MXene, the constructed MIP films were stable and highly conductive. Meanwhile, zinc-doped bismuth sulfide quantum dots (Zn-Bi2S3 QDs) were synthesized as a nano-emitter to generate strong ECL signals in the MIP film. In the sensing process, a pulsed voltage applied to the PEDOT/MXene MIP film to generate both DPV and ECL signals for simultaneous dual-mode detection. Additionally, the liquid-liquid extraction with deep eutectic solvent (menthol: octanol 1:1) was used for the pre-concentration of the BPAF in the pond mud. Based on the sensing system, the ECL and DPV response showed the good linear relationships with the concentration of BPAF with the ranges of 0.01 μM–50 μM and 0.1 μM–50 μM and the detection limits of 0.0060 μM and 0.059 μM, respectively.