In this study, a core–shell structured bimetallic nano-cube, Au@Ag NCs, was prepared by seed-mediated growth procedure. The array structure of Au@Ag NCs was achieved at the interface through the autonomous assembly technique at the three-phase boundary. Employing polydimethylsiloxane (PDMS) as a flexible carrier, the array structure was effortlessly transferred to the PDMS membrane, bypassing the need for rigid substrates through a simple “pasting” method. This yielded a highly flexible and transparent SERS substrate with an array structure (Au@Ag NCs/PDMS membrane, AAP). In order to promote the selective detection property to the practical samples, molecularly imprinted polymers (MIPs) were coated on the surface of membrane to prepare the imprinted membrane (Au@Ag NCs/PDMS-MIMs, AAP-MIMs). It was demonstrated from the results that the AAP-MIMs exhibited high SERS sensitivity, stability, and uniformity. Furthermore, the flexible substrate possessed commendable mechanical strength, and facilitated the detection of analytes on irregular surfaces. In summary, this substrate held promising potential for practical on-site detection and analysis of specific target substances.