Blending immiscible polymers provides an efficient way to obtain new materials with balanced properties. In order to optimize the final properties of immiscible blends, block or graft copolymers whose segments have diverse affinities with the components of blends are often utilized as compatibilizers to develop compatibility between phases. In this study, the dependence of compatibilization efficiency of styrene-ethylene/butylene-styrene (SEBS) triblock copolymer in immiscible polypropylene (PP)/polystyrene (PS) (20/80) blends on the preparation route was evaluated in terms of morphology, rheology and fractionated crystallization behavior. Combined experimental results with theoretical quantification, it was found that the morphology refining efficiency of SEBS showed a strong dependence on their dispersion in the blend, which could be varied by changing the mixing sequence. SEBS exhibited relatively higher compatibilization efficiency in the blends prepared by mixing SEBS and unfavorable PP in priority and the blends prepared by mixing SEBS, PP and PS simultaneously. The results were interpreted by the migration of compatibilizer during blending in which the affinity of compatibilizer with the two components and the mixing time played crucial roles. The rheology and crystallization behavior of compatibilized blends also demonstrated the similar results. It was noteworthy that the fractionated crystallization behavior of PP/PS (20/80) blends was suppressed at relatively high SEBS loadings, which could be explained by the migration of impurities from the PS phase to the PP phase promoted by the interface-located SEBS.