Oblique angle deposition (OAD) is a simple, low cost, effective, and maskless nanofabrication process. It can offer a reliable method for the mass fabrication of uniform metal nanorods which can be used as the surface-enhanced Raman scattering (SERS) substrate with an excellent enhancing performance. Up to now, Ag nanorods SERS substrates have been extensively studied. However, Ag is chemically active and easy to oxidize under atmospheric conditions. Comparatively, Au is chemically stable and has better biocompatibility than Ag. In this paper, we in detail, studied the electromechanical (EM) field distribution simulation, fabrication, and application of Au nanorods (AuNRs) on trace detection of methamphetamine. According to the finite-difference time-domain (FDTD) calculation results, the maximum EM intensity can be obtained with the length of AuNRs to be 800 nm and the tilting angle of AuNRs to be 71° respectively. The aligned Au nanorod array substrate was fabricated by the OAD process. The two key process parameters, deposition angle, and deposition rate were optimized by experiments, which were 86° and 2 Å/s, respectively. Using 1,2-bis (4-pyridyl) ethylene (BPE) as the probe molecule, the limit of detection (LOD) was characterized to be 10 M. The AuNRs were also used to detect methamphetamine. The LOD can be down to M (i.e., 14.92 pg/ml), which meet the requirements of the on-site rapid detection of the methamphetamine in human urine (500 ng/ml).