Limited knowledge of the long‐term effects of excessive iodine (EI) intake on biomolecular signatures in the liver/pancreas/kidney prompted this study. Herein, following 6 months of exposure in mice to 300, 600, 1200 or 2400 μg/L iodine, the biochemical signature of alterations to the liver/pancreas/kidney was profiled using attenuated total reflection Fourier‐transform infrared (ATR‐FTIR) spectroscopy coupled with principal component analysis‐linear discriminant analysis (PCA‐LDA). Our research showed that serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), blood urea nitrogen (BUN), serum creatinine (Scr), insulin, blood glucose levels and homeostasis model assessment for insulin resistance (HOMA‐IR) index in the 1200 and 2400 μg/L iodine‐treated groups were significantly increased compared with those in the control group. Moreover, histological analysis showed that the liver/kidney/pancreas tissues of mice exposed to EI treatment displayed substantial morphological abnormalities, such as a loss of hepatic architecture, glomerular cell vacuolation and pancreatic neutrophilic infiltration. Notably, EI treatment caused distinct biochemical signature segregation between EI‐exposed versus the control liver/pancreas/kidney. The main biochemical alterations between EI‐exposed and control groups were observed for protein phosphorylation, protein secondary structures and lipids. The ratios of amide I‐to‐amide II (1674 cm−1/1570 cm−1), α‐helix‐to‐β‐sheet (1657 cm−1/1635 cm−1), glycogen‐to‐phosphate (1030 cm−1/1086 cm−1) and the peptide aggregation (1 630 cm−1/1650 cm−1) level of EI‐treated groups significantly differed from the control group. Our study demonstrated that EI induced hepatic, renal and pancreatic injury by disturbing the structure, metabolism and function of the cell membrane. This finding provides the new method and implication for human health assessment regarding long‐term EI intake.