Attenuated total reflection‐Fourier transform infrared (ATR‐FTIR) spectroscopy is a label‐free, non‐destructive analytical technique for biochemical analysis of macromolecular components within tissue samples. Cadmium (Cd) and mono‐(2‐ethylhexyl) phthalate (MEHP), a primary metabolite of di‐(2‐ethylhexyl) phthalate, are present ubiquitously in the environment and in organisms, and have adverse impacts on ecosystems and human health. Herein we employed ATR‐FTIR analysis to identify biomolecular changes in rat liver, spleen, lung and kidney after prepubertal exposure to Cd and MEHP. Our results showed clear segregations between the 3 mg/kg Cd‐, 10 mg/kg, 50 mg/kg, 250 mg/kg MEHP‐ and binary mixture‐treated groups vs. the solvent control group. Following principal components analysis coupled with linear discriminant analysis, biochemical alterations associated with different doses of Cd and MEHP were attributed mainly to lipids, proteins, phosphates and carbohydrates. In addition, the ratios of lipid/protein, C=O stretching/CH2 methylene (lipid oxidation level), amide I/amide II, α‐helix/β‐sheet and CH3 methyl/CH2 methylene (acetylation level) in target organs were affected by these toxicants. There seems to be no dose‐response effect of Cd and MEHP on target organs. We observed hardly any joint toxic action of these toxicants. This is the first study showing the application of ATR‐FTIR spectroscopy to the assessment of toxicity of Cd and MEHP. Possibly, destruction of cell membrane structure and integrity could be the common mechanism of Cd and MEHP toxicity in liver, spleen, lung and kidney.