To manage the safety of the herbicide metazachlor, analytical methods are required for the determination of metazachlor metabolites in agricultural crops. Herein, a liquid chromatography–tandem mass spectrometry (LC–MS/MS) method was developed for the simultaneous determination of metazachlor metabolites (479M04, 479M08, and 479M16) in various agricultural commodities. After extraction using acetonitrile and adjusting the pH to 3, the samples were purified using a hydrophilic–lipophilic balance cartridge. The matrix-matched calibration curves (0.002–0.2 μg/mL) were linear (r2 > 0.99). For validation, recovery tests were carried out at three fortification levels (limit of quantification (LOQ), 10 LOQ, and 50 LOQ) in various agricultural samples. The recoveries of 479M04, 479M08, and 479M16 were 79.6–113.0, 76.9–97.7, and 79.1–102.1%, respectively, with relative standard deviation values of less than 17.0%. Furthermore, inter-laboratory testing was conducted to validate the method. All the values corresponded to the criteria of both the CODEX (CAC/GL 40-1993, 2003) and Ministry of Food and Drug Safety guidelines. Therefore, the proposed LC–MS/MS method can be used as an analytical method for the determination of metazachlor.