A terahertz (THz) metamaterial absorber based on a split ring resonator (SRR) structure was used to realize the highly accurate detection of trace pesticides, including indole-3-acetic acid (IAA) and tricyclazole. The density functional theory (DFT) was used to analysis the THz fingerprint peaks of IAA and tricyclazole. According to the dual-band (0.918 and 1.575 THz) near-perfect absorption characteristics of the absorber in the transverse magnetic (TM) polarization state, the univariate regressions were used to analyze the responses of peak amplitude and frequency to pesticide concentrations. For IAA, the sensing response based on the peak amplitude at 1.575 THz was the best with a coefficient of determination (R2) of 0.9627. As for tricyclazole, the best sensing response was based on the peak frequency at 1.575 THz with a R2 of 0.8742. Moreover, the detection accuracy of IAA (R2 = 0.9752) and tricyclazole (R2 = 0.9177) were significantly improved through effective variable selection and multivariate fusion. The results indicated that the limit of detection (LOD) of two pesticides both reached 10 ng/L. This study provided a good experimental basis for trace hazardous substances detection, presenting a new prospect for food quality and safety control in the future.