Systematic investigation on the compositional heterogeneity, phase structure, the crystallization and subsequent melting behavior of two commercial in-reactor alloys EB-P and EP-P (ethylene-co-butylene Polypropylene and ethylene-co-propylene polypropylene) from Basell were conducted. The composition of the alloys and the chain structure of each component were characterized by combinatorial using of preparative TREF and C-13 NMR technique. The compositional heterogeneities of both samples were further studied by SSA technique, and possible thermal fractionation mechanisms were then inferred. Correlations between the mechanical properties and the molecular architectures and phase structures were discussed. The results show that the excellent balance between toughness and rigidity of sample EB-P primarily benefits from the crystalline polyethylene homopolymer (HPE) phase and the amorphous ethylene-alpha-olefin copolymer (EC) component, which is proved to be enriched at the interface between the dispersed polypropylene homopolymer phase (HPP) and the matrix (HPE). As for EP-P sample, the very high amorphous EC content, and the homogeneous and interpenetrating cocontinuous phase structure in the alloy are considered to be mainly responsible for the outstanding low-temperature impact toughness.