In the present study, the model plants, arabidopsis and tobacco, were chosen for FTIR analysis to investigate the spectrum characters and the changes in their chemical component contents in the time course of HCHO treatment, providing clues to explain the difference in HCHO metabolic mechanism between the two plants. The FTIR data showed that all the chemical components of arabidopsis and tobacco varied under HCHO stress conditions. An interested peak near 1 376 cm-1 which was assigned as the absorption of methyl group of cellulose was specially existed in the spectrum of arabidopsis. This peak showed a mild decrease compared with other peaks at the beginning (at 1 day) of HCHO stress. This indicated that the major part of HCHO metabolic flux was introduced towards its oxidation pathway to form HCOOH and CO2 subsequently and only small amount of HCHO entered the other pathways. The CO2 was assimilated in Calvin cycle to form sugars which might be used to synthesis of cellulose later. At 7 day of HCHO treatment, the height of the peak decreased whereas the height of the other peaks still increased. This might suggest that the gene expression of some enzymes in the HCHO oxidation pathway was inhibited under HCHO stress conditions and the inhibition might not happen to the gene expression of the enzymes in other pathways. In the case of tobacco, the contents of all chemical components showed the same variation on the FTIR spectrum in the time course of HCHO treatment, which indicated that there was no much difference in HCHO metabolism flux in each pathway. At 4 day of HCHO treatment, the decrease in the height of all peaks is the result of the poor ability of HCHO metabolism of tobacco, which also demonstrated the lower HCHO tolerance of tobacco compared with arabidopsis.