This work focuses on the effect of the unique molecular structure of OBC (olefin block copolymer) constituted by soft blocks and hard blocks on the compatibility of OBC/iPP (isotactic polypropylene) blends. Two OBCs with high and low octene content were selected to blend with iPP. The thermal behavior, morphology, and kinetics of crystallization of the binary blends were studied systematically. The variation in octene content of the OBCs caused a dramatic difference in their own mesophase separation as well as their compatibility with iPP in blends. As the octene content increased, mesophase separation of OBC became more and more dominant, with the strong repulsive interaction between the hard and soft blocks of OBC and the coupled fact that the majority of the soft blocks are more compatible with iPP, resulting in its better compatibility with iPP. This was proved by smaller dispersed domain size, better interfacial adhesion, and faster crystallization kinetics, On the other hand, we also found that annealing time was important in controlling the superstructure in blends. There is a possible scalability of the mesophase separation of OBC on the compatibility and superstructure of the OBC/iPP binary blends. According to our results, it is reasonable to obtain a systematic profile to adjust the compatibility as well as the superstructure to satisfy different mechanical requirement by regulating octene content in the OBC and the annealing condition of the blends.