Resource mining provides a solid foundation for China's rapid economic growth. However, mining activities also lead to various environmental issues, such as wastewater discharge, soil contamination, and air pollution. Under these resource and environmental constraints, it is critical to quantitatively evaluate the ecological loss caused by mining activities and to determine the appropriate values on ecological compensation. Many evaluation methods are in use to assess the comprehensive performance of this sector, such as material flow analysis, life cycle analysis, and substance flow analysis. However, these traditional methods cannot mimic the real contribution of local ecosystems since they focus on individual aspects of resource use and system metabolism and discard other parameters and driving forces. In addition, they do not account for the value of existing natural capital, leading to incomplete assessments of the whole system. In addition, these methods lack the ability to address waste and emission management, as well as recycling strategies, resulting in policies optimizing one individual resource or flow, rather than tracking diverse, non-linear interactions between human society and the natural system in which economic processes are embedded. Emergy analysis provides a "supply-side" evaluation by focusing on nature's investment, and can assign environmental impacts more fairly, discouraging inefficient and unnecessary resource depletion. By quantifying both the direct and indirect environmental costs of resource mining, and related waste management and disposal, emergy analysis is a suitable approach in assessing the overall performance of the mining sector, leading to accurate decision-support and integrated measures on protecting mining resources. In this study, China's non-ferrous metal mining sector was examined to detect direct and indirect losses caused during the mining processes by employing emergy analysis. An Ecological Compensation Index (ECI) was developed in order to provide rational references for determining ecological compensation standards. Our results indicate that, from the perspective of sustainable development, the ECI was 89.18%, indicating that more renewable resources have been input into the non-ferrous metal mining sector, and more money is needed for ecological compensation. The Emergy Yield Ratio (EYR) was 9.24, indicating that the production efficiency of the non-ferrous metal mining sector was greater, whereas the Environment Loading Ratio (ELR) was 238, indicating a greater environmental load on the surrounding ecosystem. The Emergy Index of Sustainability (ESI) was 0.039, indicating that the system was unsustainable, and there is a need to adopt appropriate environmental protection measures. From an economic perspective, the ecological compensation value for the non-ferrous metal mining sector should be 438 million Chinese Yuan (CNY). However, the current resource tax is far less than the real expense for ecological remediation and cannot cover its treatment costs. Finally, policy implications at the macro-, micro-, and long-term levels increased in order to address the main problems that China's non-ferrous metal mining sector is facing. For instance, the overall development strategies on the non-ferrous metal mining sector should move from the traditional "end-of-pipe" treatment toward source control. Pollution prevention-oriented approaches, such as wastewater reuse/recycling, brownfield redevelopment, and the collection and recycling of discarded non-ferrous metals, should be promoted so that the overall extraction and processing of original non-ferrous metals can be reduced, and the corresponding environmental emissions can be mitigated.