In this study, blend nanocomposites of polylactic acid (PLA), poly[(butylene adipate)-co terephthalate] (PBAT), and nanoclay (Cloisite 30B) were prepared through twin-screw extruder (TSE). Two different PLAs with low and high D-lactide contents (semi-crystalline and amorphous, respectively) were used as the matrix phase in blend systems. The processing was conducted at 180oC and 100 rpm and the results were compared with those obtained from internal mixing of a previous work that was conducted at 160oC, 100 rpm where mixing time was10 min. The effects of two major mechanisms (thermodynamics and kinetics) on the selective localization of nanoclay in matrix, second polymer phase, or phases interfaces were explored. To thermodynamically predict the morphology of the blend nanocomposites, interfacial tension between each two phases and the wetting coefficient values were calculated. The morphology of the blend systems was explored through using scanning and transmission electron microscopies (SEM and TEM). Subsequently, the materials and morphological variation influences on the thermal, crystallization, and mechanical properties of blends were investigated and compared, respectively, using dynamic mechanical analysis (DMA), differential scanning calorimetry (DSC), and tensile testing. The results revealed that the nanoclay particles are thermodynamically preferred to be localized mainly at the phase interfaces of PLA and PBAT and then the excessive particles could prefer to be located in PLA. The properties were also varied differently based on the obtained blend morphology.