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Deoxycholate (DA) is a natural emulsifying agent involved in the absorption of dietary lipids. Due to the facial distribution of hydrophobic-hydrophilic region, DA easily aggregates under ambient conditions, and this property hinders the practical application of DA in clinical applications. In this study, we found that the molecular arrangement of DA molecules could be controlled by using layered double hydroxide (LDH) under a specific reaction condition. The effect of reaction methods such as co-precipitation, ion exchange and reconstruction on the molecular arrangement of DA was investigated by X-ray diffraction, Fourier-transform infrared spectroscopy, high-resolution transmission electron microscopy and differential scanning calorimetry. It was demonstrated that the self-aggregation of DA molecules could be suppressed by the oriented arrangement of DA between the gallery space of LDH. The DA moiety was well stabilized in the LDH layers due to the electrostatic interaction between DA molecules and LDH layers. The most ordered arrangement of DA molecules was observed when DA was incorporated into LDH via a reconstruction method. The DA molecules arranged in LDH via reconstruction did not show significant exothermic or endothermic behaviour up to 400°C, showing that the DA moiety lost its intermolecular attraction in between LDH layers.