A rapid, accurate and novel detection method of plant hormones abscisic acid at ultra-low concentrations in wheat leaves was proposed in this study. This surface-enhanced Raman spectroscopy based method developed the substrate with the silver coated gold nanocomposites. This substrate exhibited excellent detection of rhodamine6G with an ultra-low concentration of 1 × 10−12 M. And resulted in high-performance, well homogeneity and reproducibility against abscisic acid hormone detection with a limit of detection of 1 × 10−9 M. This assay further measured abscisic acid hormones from the fresh leaves extract of wheat with the relative error of 3.72–10.66% compared with enzyme-linked immunosorbent assay bioassay.