In the present paper, the authors reported the assembly and SERS studies of a simple device unit of a metal nanowire-molecule-metal nanoparticles junction in an anodic aluminum oxide (AAO)template. The AAO template was fabricated by two-step electrochemical oxidation. Metals were filled into the pores by AC deposition. Then the AAO template with metal nanowires was immersed into the solution of 1,4-benzenedithiol (1,4-BDT), which was followed by the immersion into silver nanoparticles with appropriate diameter. 1,4-BDT served as the probe molecule for SERS detection as well as the molecule for linking the metal nanowires and metal nanoparticles. The simple junction of metal-molecule-metal embedded in AAO template was built successfully. The SERS effect of the junction was investigated through the dissolution of AAO template to expose the junctions in the same orientation (standing on the substrate vertically). The giant enhancement from the former junction might be attributed to the coupling effect in the junction. The authors’ preliminary results revealed that SERS might be a characteristic tool for the junction and the construction on the junction will be beneficial to the investigation of the complex SERS mechanism.