Chlorothalonil is an organochlorine fungicide that blocks the respiratory process of cells and persists in agricultural products because it is used extensively to prevent fungal diseases. An analytical method of chlorothalonil using the modified QuEChERS method and gas chromatography- mass spectrometry (GC-MS/MS) was developed to analyze the residue in agricultural commodities distributed in Republic of Korea. Acetonitrile, including acetic acid and formic acid, was used to compare the extraction efficiency. The extraction and purification processes were established by comparing three versions of the QuEChERS method and various dispersive solid-phase extraction (d-SPE) combinations. Ultimately, 1% formic acid in acetonitrile with QuEChERS original salts and d-SPE (PSA, C18) were selected for the extraction and clean-up procedures for method validation and establishment. Five agricultural commodities, viz., brown rice, mandarin, soybean, pepper, and potato, were examined to validate the established method, which displayed excellent linearity, with a coefficient of determination of R2 = 0.9939-0.997 in the calibration curve range of 0.002-0.1 mg/kg. The limits of detection (LOD) and quantification (LOQ) were calculated to be 0.003 mg/kg and 0.01, respectively, for the method. The LOQ value satisfied the suitable level for the Positive List System (PLS). The mean recovery of chlorothalonil was 79.3-104.1%, and the coefficient of variation was <17.9% for intra- and inter-day precision at 0.01, 0.1, and 0.5 mg/kg. The matrix effects in the five commodities were confirmed by the ion suppression effects, except for brown rice, in which a medium enhancement effect was observed at 21.4%. Chlorothalonil was detected in eight apples, one watermelon, and one cucumber. Ultimately, chlorothalonil was detected in ten agricultural products. Thus, this analytical method could be used for the routine detection of chlorothalonil in agricultural products, and the data may be used to inform and improve current food policies.