The structural difference of the interface between polypropylene pair (PP/PP) and polypropylene and poly(ethylene-alt-propylene) pair (PP/EAP) was investigated using molecular dynamics and molecular mechanics, under a two-dimensional periodic boundary condition (2DPBC). From the position of the end group of each polymer chain, the influence of the chemical structure and the mobility of the polymer chain were considered. In the PP/PP system, the end group is mainly located in the middle region of each polymer layer. In the PP/EAP system, the PP end group and the ethylene end group of EAP are also located in the middle region of each polymer layer, but the propylene end group of EAP is located very near the interface. These results suggest that the mobility of the middle part of the polymer chain is not so small, and that the similarity in the chemical structure, which is a measure of the interaction strength between polymers, plays an important role in the early stage of adhesion. An easy and efficient estimation method of the interaction strength between polymer pairs is also proposed, and the influence of the component sequence in copolymer on the interaction strength is systematically estimated.