Due to swelling, smectite minerals are capable of intercalating many organic molecules in their interlayer space. Tetracycline (TC) is a group of antibiotics used extensively in human and veterinary medicine. The great aqueous solubility and long environmental half life of TC mean that the study of interactions between swelling clay minerals and TC are of great importance in TC transport and retention in subsurface soils. In the present study, the intercalation of TC molecules at different levels into smectites was investigated using Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD). The shift of the FTIR bands of amide I and II in comparison to crystalline TC suggested a strong interaction between the amide groups and the clay surfaces. The band at 1455 cm−1 remained the same after TC intercalation into SAz-1, SWy-2, and SYn-1, suggesting that complexation was not a dominant mechanism of TC uptake by these minerals. With cation exchange as the major mechanism of TC intercalation into these minerals, simultaneous removal of H+ from solution protonated the TC molecules and provided a positive charge to interact with negatively charged mineral surfaces even in neutral to slightly alkaline conditions. The increase in interlayer distance after intercalation by TC, as revealed by XRD, suggested a tilted orientation of the intercalated TC molecules in both twisted conformation in acidic condition and extended conformation in alkaline condition.