To find out the toughening mechanism of in-situ toughening telechelic polymers (ITTP) in concrete, SEM & EDS and Nano indenter were used to research the variation of concrete hydration products and the interfacial transition zone between the cement paste and aggregate. The results indicate that the toughening effect of ITTP is not carried out by film formation. And the proportion of LD C-S-H in cement hydration products increased significantly and the CH content decreased after introducing the ITTP into concrete. Nano indentation test results show that the non-dense area ratio of ITZ decreased, and the CH content in ITZ increased slightly. The Ca/Si blurred from mutation pattern with decreasing the distance to aggregate surface in the region of interfacial transition zone between aggregate and cement paste, and the thickness of ITZ increased. The conclusions show that the ITZ and hydration products are both key micro-structures which affect the toughness of concrete, and it provides us some guidance for realizing concrete toughness ascension through microstructure adjustment.