The catalytic activity and selectivity of heterogeneous catalysts are governed by atomic and electronic structures at the heterointerface between noble metal nanoparticles (NPs) and oxide substrates. In specific chemical reactions, it is well-known that the catalytic activity is strongly suppressed by annealing in a reducing atmosphere, so-called strong metal-support interaction (SMSI). However, it is still unclear the formation process and atomistic origin of the SMSI. By preparing well-defined platinum (Pt) NPs supported on atomically flat TiO2 (110) substrate, we directly show the formation of chemically ordered Pt-Ti intermetallic NPs and impregnation of NPs into TiO2 substrate at high temperatures by using atomic-resolution scanning transmission electron microscopy combined with electron energy-loss spectroscopy. Furthermore, we observed negative charge transfer from the Pt-Ti intermetallic NPs to the TiO2 surface, which would strongly affect the catalytic activities.