Microscopic studies on the deformation mechanism of the blends of polyamide6 (PA6) and polycarbonate (PC) compatibilized with triblock copolymer of poly[styrene-b-(ethylene-co-butylene)-b-styrene] (SEBS) functionalized with maleic anhydride (SEBSgMA) were carried out. As described in our previous paper, significant improvement of mechanical properties of this blend series can be achieved by the use of the combination of SEBSgMA and unmodified SEES (unSEBS) as compatibilizers. Especially, when the composition of the blends of PA6/PC is 75/25 and the total amount of added SEES is 20 phr, drastic enhancement of the impact strength and of the elongation at break in the tensile stress-strain tests can be achieved by varying the ratio of SEBSgMA to unSEBS. The encapsulation by SEES on the PC domains gradually become incomplete as the increase of the ratio of unSEBS to SEBSgMA and then the mechanical properties can be maximized. We observed the deformed zone of the specimens loaded to the tensile stress-strain tests and to the Izod impact tests using transmission electron microscopy (TEM) in order to find out the origin of this enhancement of the mechanical properties. It has revealed that voids tend to be generated at the PA6/PC interface easily due to the incompletion of the encapsulation achieved by the use of the combination of SEBSgMA and unSEBS, and thereby the local shear yielding of the matrix is promoted to dissipate the tensile and the impact energy.