The sustainable development of hydropower megaproject (HM) is a crucial component of sustainable water resources management within the river basin. Hence, quantitatively appraising the multiple losses caused by construction and operation on HM sustainability is a critical and complex task. This study proposed an emergy-based sustainability evaluation model incorporating the social-economic-ecological losses (ESM-SEEL), integrating the SEEL during the construction and operation of the HM system into the emergy calculation account. The Three Gorges Project (TGP) was selected as a case study, and the comprehensive evaluation and comparative analysis of the temporal evolution and sustainability characteristics of the TGP system from 1993 to 2022 was carried out. The results showed that: 1) The inflow runoff chemical potential emergy (2.77×10²⁴sej) and the emergy losses (1.48×10²⁴sej) are the primary input sections of the TGP system, accounting for 52.1% and 27.9% of the total emergy inputs, respectively. The flood control function of the TGP has generated significant socio-economic benefits (1.27×10²⁴sej), accounting for 35.2% of the total emergy output. 2) The resettlement compensation, water pollution during operation, fish biodiversity loss, and sediment deposition are the main losses of the TGP, accounting for 77.7%, 8.8%, 5.5%, and 2.5% of the emergy losses, respectively. 3) The emergy-based sustainability assessment indicators showed that the sustainability level of the TGP is increasing, and the improved emergy sustainability index (IESI) is consistent with the actual situation of the TGP and the drought-flood years in the Yangtze River basin. IESI values are higher (lower) in years characterized by abundant (insufficient) river runoff. Therefore, along with maximizing the benefits of the HM system, reducing the HM system's losses is a critical approach to coordinate the hydropower development and ecological environment in the Yangtze River basin. This study helps to understand the complex relationship between people and water and provides theoretical guidelines and scientific foundations for the sustainability assessment of hydropower.