It has great significance to research the effect of intercalated molecules with the same carbon chain and different functional groups on the properties of intercalation compounds since it can reveal the effect of different functional groups on the properties of intercalated compounds without considering the difference of carbon chains. In this study, the intercalation compounds of kaolinite/dodecyl trimethyl ammonium chloride (Kaol-DTAC) and kaolinite/dodecylamine (Kaol-DA) were studied by using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), thermogravimetry and differential scanning calorimetry (TG-DSC) analysis, and Scanning electron microscope (SEM). Then the de-intercalation kinetics with different heating rates was investigated, and the optimized the mechanism function for de-intercalation process was calculated. The results showed that the basal spacings of Kaol-DTAC and Kaol-DA intercalation compounds are 3.56 and 4.08 nm, respectively. The DTAC molecules are arranged the Kaol surface in a single layer with an angle of 90° while the DA molecules are tilted towards the Kaol surface in bilayer and the inclination angle is 39.9°, which is due to the different structure between these two type molecules. The SEM showed that the ratio, nanoscrolls length to diameter, of Kaol-DA is larger than that of Kaol-DTAC, and for the yield of nanoscrolls, the former is greater than the latter. Moreover, by using KAS and Ozawa methods, the activation energy (E) of Kaol-DTAC and Kaol-DA were obtained and the average values are 102.44 kJ mol−1 and 130.80 kJ mol−1, respectively. Furthermore, The optimal mechanism function for the intercalation compounds of Kaol-DTAC and Kaol-DA are G(α) = -ln(1-α) and G(α) = [(1-α)(−1/3)−1]2, respectively.