Adding nanofillers Cloisite 30B (C30B) and Cloisite 15A (C15A) to poly(ethylene terephthalate) (PET)/poly(ε‐caprolactone) (PCL) (70/30, wt/wt) blends via melt blending can improve their phase morphology and change their interface properties. The effects of the different selective localization of clay on the structure and the morphologies are studied and evaluated by theoretical and experimental methods. It is found that C30B is selectively localized in PET and at the PET‐PCL interface, whereas C15A is mainly localized at the interface. Moreover, the changes in the rheological behavior of the blends are attributed to the formation of clay network‐like structures. X‐ray diffraction, scanning electron microscope, and transmission electron micrograph observations also evidenced an exfoliated and/or intercalated structure of C30B, and intercalated structure of C15A in the blend, together with significant morphology changes of the initially immiscible blend. The relative permeability to PET/PCL of the nanocomposites decreased with the increasing of nanoclays content. © 2020 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020, 137, 48812.