This study performs a novel examination of the gas transport properties in the poly(lactic acid)/montmorillonite (PLA/MMT) interface layer by comparing the permeation parameters of dry gases and those dissolved in water. Furthermore, the relationship between the transport properties of oxygen and carbon dioxide in the gas and water phases and the crystallinity/crystal structure of the PLA/MMT composite films prepared by varying the MMT content in the PLA polymer and cooling conditions was systematically investigated. The results showed that the crystallinity of the PLA/MMT composite film increased with decreasing cooling rates, while the oxygen and carbon dioxide permeabilities increased with increasing MMT content and crystallinity. A small continuous space of size ranging from a few nanometers to a few dozen nanometers wherein the gas molecules easily diffuse around the interface might be formed between the crystalline and amorphous regions, which could not be observed by microscopic analysis. This interfacial space caused an increase in the selective permeation of carbon dioxide, which exhibits higher solubility in water, and the selective elimination of oxygen, which exhibits lower solubility in water.