This paper presents the fabrication of a molecularly imprinted, polymer-based disposable electrochemical sensor for paraoxon (PO) determination. The sensor was based on a screen-printed carbon electrode (SPCE) modified with a surface molecularly imprinted poly (p-aminothiophenol) (PATP)/gold nanoparticles (AuNPs) composite film, which consisted of a PATP outer layer and an AuNPs inner layer. We report a novel strategy, combining surface molecularly imprinting and self-assembly directed electro-polymerization with high densely imprinting PO molecules in the PATP/AuNPs film. Firstly, AuNPs were in situ electrodeposited at the electrode surface, and then assembled with electropolmerizable functional monomer p-aminothiophenol (ATP). Subsequently, PO molecules were assembled onto the ATP monolayer-modified AuNPs, forming a basis of surface molecular imprinting. After that, replenished PO molecules were embedded in the PATP/AuNPs film by PO and the ATP molecular self-assembly directed electro-polymerization in the polymerization precursor mixture. The resulting imprinted PATP/AuNPs/SPCE possesses high sensitivity, affinity, and selectivity toward PO, with a low detection limit of 1 × 10−9 M. The proposed sensor was successfully applied for the determination of PO in fruit and vegetables, giving satisfactory recoveries. The strategy reported herein can be further expected to fabricate various molecular imprinted sensors for the determination of other pesticide residuals.