Magnesium phosphate cement (MPC) as a fast-setting material has been widely used in the rapid repair of cement concrete pavement. A decisive role was played in the bonding performance of the repair interface between MPC and portland cement concrete (PCC) except for the high early strength and good durability of MPC. Premising the MPC as the rapid repair material for PCC, the characterization and analysis of the interface performance are studied. The data of elastic modulus for the interfacial transition zone (ITZ) is measured by nanoindentation technology while the mechanical properties firstly. The heterogeneity and stratification in the ITZ were characterized by the combination of Raman spectroscopy and nanoindentation test. The content of each material composition was explored with scanning electron microscopy (SEM) and energy-dispersive spectrometer (EDS) experiment and X-ray diffraction (XRD) analysis. Additionally, the adhesion-like substances in the cracks, observed by SEM images in the ITZ, inferred a certain self-healing ability of the polymer-modified magnesium phosphate cement (PMPC). Finally, the elastic modulus of ITZ was simulated by DIGIMAT version 2019.1 software, indicating that the single-layer microstructure analysis is feasible for obtaining elastic modulus of the ITZ without hydration stratification, while the multilayer microstructure analysis is necessary for obtaining elastic modulus of the ITZ with the hydration stratification.