We have studied the intercalation of cationic surfactant cetyltrimethylammonium (C16TMA) into the interlayer of synthetic layered silicate, Na-magadiite in the presence of different anions. The amount of intercalated C16TMA cations depends on the anion types, with a maximum of 1.16 mmol/g achieved. The raw Na-magadiite exhibited a basal spacing of 1.54 nm that increased up to 3.12 nm after intercalation of C16TMA cations. A reflection at 1.54 nm was also observed and could be to non-exchangeable Na-magadiite or a second-order reflection of 3.12 nm phase. The intercalation of C16TMA cations into H-magadiite was studied to identify the type of 1.54 nm reflection. The 13C CP/MAS NMR indicates that the intercalated surfactants exhibit a homogeneous trans conformation similar to the starting C16TMABr. The in situ powder X-ray diffraction was performed to confirm the complete exchange reaction of Na-magadiite with C16TMA cations, and to study the thermal stability of these materials. At intermediate heating temperature of 100–150 °C, the basal spacing of 3.12 nm shifted to 3.36 nm. At heating temperature above 220 °C, the layered structure collapsed due to the decomposition of surfactant, independent of the heating atmospheres air or nitrogen.