This paper reports the surface treatment of layered double hydroxide (LDH) by using ionic liquid (IL) composed of phosphonium cation combined with 2-ethylhexanoate (EHT) counter anion as surfactant agent. Then, different amounts (1, 3, 5 and 7 wt %) of thermally stable organically modified LDH (up to 350 °C) denoted LDH-EHT were incorporated into polycaprolactone (PCL) matrix by mechanical milling. The influence of LDH-EHT loading has been investigated on the physical properties, such as the thermal and barrier properties, as well as the morphologies of the resulting nanocomposites. Thus, intercalated or microcomposite morphologies were obtained depending on the LDH-EHT loading, leading to significant reduction of the diffusion coefficient respect to water vapor. The modulation of barrier properties, using low functionalized filler amount, is a very important aspect for materials in packaging applications.