Reinforced concrete structures need to be repaired after exposure to fire, in which the weakness of the interfacial transition zone between the repair mortar and the old concrete substrate is a crucial problem. Carbon nanotube can be added into repair mortar to address the above-mentioned problem because of its bridging, pore filling and nucleation effects. However, the bonding mechanism of functionalized carbon nanotube repair mortar and the old concrete is not yet fully understood. Therefore, this study investigates the bonding performance between different functionalized carbon nanotube repair mortar and old mortar substrate exposed to high temperature. Firstly, to evaluate the roughness of old mortar exposed to high temperature, three-dimensional microscope and mercury intrusion porosimetry were performed in this paper. Secondly, thermogravimetric analysis and X-ray diffraction were carried out to further analyze the phase composition of the repair mortar. Thirdly, microstructure of the interfacial transition zone was investigated by electron backscatter diffraction characterization and microhardness measurements. Fourthly, the bonding mechanism of interface between new and old mortar was discussed. The results show that the surface roughness of the old mortar can gradually increase with increasing of temperature, which improves the interfacial mechanical interlocking. The functionalized carbon nanotube can reduce the content and orientation of calcium hydroxide and improve the microhardness of the interfacial transition zone. Finally, an interfacial bonding strength prediction model considering porosity and the reinforcing effects of different functionalized carbon nanotube is proposed. The findings of current study can benefit further research and application of nanomaterials in the field of structural repair and maintenance.