3-Chloro-1,2-propandiol (3-MCPD) dipalmitate is one of the major 3-MCPD esters formed during food processing. In this single-dose study, the metabonomic profile changes in the 48 h after orally administrated 3-MCPD dipalmitate at 1600 mg/kg BW to Sprague-Dawley (SD) rats were determined with liquid chromatography (LC) coupled with mass spectrometry (MS) system. The chemical structures of 12 potential biomarkers for 3-MCPD dipalmitate exposures early detection were detected and tentatively identified from the plasma of SD rats, including indoxyl sulfate, phenol sulfate, p-cresol sulfate, 2-phenylethanol glucuronide, p-cresol glucuronide, p-cresol, allantoin, phenylacetylglycine, pyrocatechol sulfate, phenyllactic acid, 5-hydroxyindoleacetic acid, and creatinine. Taking into account the metabolites identified from SD rats' kidney, liver, testes, and spleen samples, 3-MCPD dipalmitate might potentially disturb the phenylalanine, tryptophan, tyrosine, glycine, fatty acid, and purine metabolisms. The results suggested that the 12 plasma metabolites could be potentially applied in detecting the early exposures of 3-MCPD esters.