This study presents a novel sandwich composite structure that was designed for the ultra-sensitive detection of cyclotrimethylenetrinitramine (RDX). Au nanorod arrays (Au NRAs) were prepared and bound to 10-7 M 6-MNA as adsorption sites for RDX, while Au nanorods (Au NRs) were modified using 10-5 M 6-MNA as SERS probes. During detection, RDX molecules connect the SERS probe to the surface of the Au NRAs, forming a novel type of Au NRAs-RDX-Au NRs "sandwich" composite structure. The electromagnetic coupling effect between Au NRs and Au NRAs is enhanced due to the molecular level of the connection spacing, resulting in new "hot spots". Meanwhile, Au NRAs and Au NRs have an auto-enhancement effect on 6-MNA. In addition, the presence of charge transfer in the formed 6-MNA-RDX complex induced chemical enhancement. The limits of detection (LOD) of RDX evaluated by Raman spectroscopy using 6-MNA were as low as 10-12 mg/ml (4.5×10-15 M) with good linear correlation between 10-12 and 10-8 mg/ml (correlation coefficient R2 = 0.9985). This novel sandwich composite structure accurately detected RDX contamination in drinking water and on plant surfaces in an environment with detection limits as low as 10−12 mg/ml and 10−8 mg/ml.