One of the most challenging and still unsolved problems within the design and operation of composite structures is the prediction of its behavior under fatigue loading. This problem is even more complex when a composite structure contains damage, especially low-velocity impact damage considered as one of the most dangerous types of damage in composite structures. In this paper, the authors presented the hybrid method, which combines the evaluation of a fatigue limit of structures with low-velocity impact damage (LVID) with a non-destructive evaluation of this damage using thermocouples and thermography in a single test. The tests were performed on carbon and glass fiber-reinforced composite structures with LVID of various energies. The relation between fatigue limit and impact energy was demonstrated, and the observed damage mechanisms analysis was performed. Moreover, the performance of LVID detectability is analyzed, defining minimal self-heating temperature increase necessary for detection of LVID. The proposed method demonstrated high sensitivity to impact damage and simultaneously an ability of evaluation of fatigue life of a tested structure. Finally, the recommendations on measurement setup and parameters of testing are provided. It was demonstrated that the proposed hybrid method could be successfully used for rapid, precise and non-destructive evaluation of residual life of composite structures after impact loading.