The objectives of this study are to investigate the possible occurrence status of formamide in the intercalation system, the founction of water and the molecular configurations and orientations of formamide inserted into the interlayer of kaolinite, by washing the products with acetone to eliminate the interferences due to the outersurface absorbed formamide molecules in FTIR spectrometry. The results show that the intercalated, absorbed and free formamide probably exist in the intercalation system. Free formamide is easily to be eliminated selectively by drying, whereas the absorbed formamide is removed only by washing with the proper eluting reagent. H2O also is inserted into the interlayer during the formamide molecules’ intercalation, which is deintercalated after the compounds being dried. Intercalation caused blue shifts of the inner surface OH stretching bands from 3 687 to 3 692 cm-1, and deforming bands from 911 to 906 cm-1 , the bands at 3 651 cm-1 disappeared with a new band appearing at 3 539 cm-1. The frequency of the Si—O bands of kaolinite was slightly shifted. These IR bands changes implied the breaking of the H-bonds between layers of kaolinite, and the formation of new H-bonds between the kaolinite and the inserting formamide molecules in the intercalation compounds. The formamide molecules intercalated were oriented with the C—N bond perpendicular or nearly perpendicular to the (001) surface of the kaolininte and formed 2 types of H-bonding with inner-surface hydroxyls and siloxane layer of the kaolinite respectively through NH2. A novel model was provided to analyse the microstructure of kaolinite-formamide intercalation compounds. The results show that computation data is in good agreement with experimental data.