The connection between aircraft composite panels and metal panels is an important research topic in the fuselage structure design. Due to the differences in properties between composites and metals, resulting in the stress of hybrid connectors during service being difficult to predict. Novel carbon nanomaterials represented by carbon nanotubes (CNTs) and MXene films possess unique nanoscale structures and excellent physical properties. In this paper, by improving the preparation process of MXene/CNT composite film sensors and applying them to the health monitoring of composite/metal joint structures, a whole process tracking test of the hybrid joint structures during service is carried out. The results show that the monitoring responses of the thin film sensor throughout the process coincide with the stress–strain curve of the hybrid structure connectors, and it can give accurate early warnings of the failure of the hybrid connection structure, which has certain engineering significance.