The development of sensitive and selective methods for detecting pesticide residues has become paramount for ensuring food safety. In this work, a high-performance molecularly imprinted electrochemical sensor based on the composite of Cu-BTC- and FeCo-ZIF-derived N-doped carbon (FeCo@NC), synthesized by pyrolysis and electrodeposition, was developed for Benomyl (BN) detection. The materials were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS). In this sensing system, the Cu-BTC/FeCo@NC composite used as the electrode substrate displayed a large specific surface area, high electronic conductivity, and rich active catalytic sites, demonstrating excellent electrocatalytic ability toward BN oxidation. Meanwhile, Cu-BTC, with its abundant surface functional groups, facilitated strong hydrogen bonding interactions with the imprinted template molecule of 3,4-ethylenedioxythiophene (EDOT), promoting the formation of a uniform molecularly imprinted membrane on the substrate material surface. The introduced MIP-PEDOT could enhance the selective recognition and enrichment of the target BN, leading to an amplified detection signal. Thanks to the synergistic effects between Cu-BTC/FeCo@NC and MIP-PEDOT, the proposed sensor achieved a low detection limit of 1.67 nM. Furthermore, the fabricated sensor exhibited high selectivity, reproducibility, and interference resistance in detecting BN. The method has been successfully applied to the determination of BN in vegetable and fruit samples, indicating its potential for use in practical applications.