Abstract: The ground motion duration plays a crucial role in structural damage evaluations and in post-earthquake loss assessments. However, there is a lack of unified definitions of cumulative damage in structural degradation quantifications and in seismic performance classifications. Existing studies on this issue focus on peak-based demand parameters, which are insufficient to capture the cumulative damage induced by ground-motion duration. To address this limitation, this study establishes a relationship between the maximum inter-storey drift and an energy-based damage index based on the displacement-energy transformation framework. A probabilistic capacity model centered on structural energy dissipation is then developed, enabling the transformation of structural capacity models and damage thresholds from peak-based parameters to energy-based parameters. Two five-storey reinforced concrete frames with different seismic design levels are selected as case-study structures. A total of 140 pairs of spectrally matched long- and short-duration ground-motion records are employed to investigate the effects of ground-motion duration on structural seismic responses, on fragility and, on economic losses. The research results indicate that long-duration ground motions significantly increase the probability of structural failure, with the failure probability under long-duration excitations reaching up to 10 times that under short-duration excitations. Moreover, the amplification becomes increasingly significant with the progression of damage severity, exhibiting a clear “damage-state dependency”. The results of an economic loss analysis further reveal that long-duration ground motions markedly increase both direct and indirect economic losses. Specifically, the direct economic losses under long-duration excitations are approximately 1.5-2.4 times those under short-duration excitations, while indirect economic losses are about 2.1-2.6 times larger. The indirect economic losses demonstrate a higher sensitivity to ground-motion duration than those of the direct losses. In addition, the loss amplification tends to diminish with increasing seismic design levels of the structures. Overall, this study demonstrates that: the proposed energy-based probabilistic assessment framework provides a more rational method for the structural performance degradation and loss evolution under long-duration ground motions, and more effectively evaluates the potentially negative influence of ground-motion duration on structural functional recovery and seismic loss assessments.