Thermally induced lamellar structure changes due to phase transition and degradation in organoclays based on a synthetic ‘Somasif’ mineral and two organic surfactants, di-methyl dihydro-ditallow ammonia chloride (DMDTA) and tri-butyl-hexadecyl phosphonium bromide (HTBP) were investigated by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), Fourier transform infrared (FTIR) spectroscopy, in situ simultaneous small-angle X-ray scattering (SAXS) and wide-angle X-ray diffraction (WAXD) over the temperature range 30–280°C. Results indicated that the surfactant layer in ‘Somasif’-based organoclays underwent thermally induced melting-like order-disorder transition followed by desorption of surfactant molecules, resulting in drastic changes in the character of the layer periodicity. The transition temperature (Ttr), determined from the endothermic transition in DSC, was found to depend strongly on the type and the content of surfactant incorporated. Temperature-resolved SAXS indicated complex intercalated layered structures, containing multiple lamellar stack populations of two different organic layer thicknesses. A weak scattering peak (s0), located at exactly the half angular position of the strong first scattering maximum s1 (s0 = 0.5s1), was found in all tested ‘Somasif’ clays. The presence of this peak can be attributed to a slight breaking of the translational symmetry in the layered structure, causing the 1D repeat period in real space to be doubled. In other words, some portions of layers are grouped into pairs and a single pair forms the new repeat unit. This arrangement is reminiscent of the Peierls-like distortion.