This study concentrated on evaluating the structure-property correlation of two polypropylene/poly (ethylene-co-propylene) in-reactor alloys (A and B). Systematic investigation and comparison have been performed on the molecular structure and phase morphology of the polypropylene (PP)-based alloys. Especially, the bivariate distribution of chemical composition and molecular weight for each fraction was obtained simultaneously by adopting cross fractionation chromatography. The results illustrated the following structure difference which determines the ultimate mechanical properties of the PP in-reactor alloys. It has been found that the relative content of components polypropylene homopolymer (HPP) and ethylene-co-propylene random copolymer (EPR) is a little more in sample A than those in sample B, and meanwhile both of them in sample A show higher molecular weight and broader molecular weight distribution. Furthermore, the fraction of HPP in sample A eluted at a higher temperature, meaning that this fraction possesses better stereo-tacticity and can form more perfect crystals with higher crystallinity. These advantages in structure characteristics endow sample A with better rigidity-toughness balance than sample B.