Two methods of natural ecosystem assessment—emergy analysis (EMA) and life cycle assessment (LCA)—are reviewed in this paper. Their advantages, disadvantages, and application areas are summarized, and the similarities and differences between these two evaluation methods are analyzed respectively. Their research progress is also sorted out. The study finds that EMA and LCA share common attributes in evaluation processes and research fields, but they focus on different aspects of macrocosms and microcosms. The assessment of system sustainability is valued by both EMA and LCA, but the former has unique advantages in natural system input analysis, and the latter is more convincing in assessing environmental loading capacity. If the system boundaries of the two methods are expanded, in other words, factors such as ecosystem services, labor, and infrastructure construction are integrated into the upstream of the target system, and environmental impact is further analyzed using LCA in the downstream of the system, the two approaches would complete each other. The quantified results would be more objective. Therefore, these two theories have the necessity of coupling development. After reviewing recent coupling application cases, the results show that LCA and EMA have commonality in the upstream of the target system (mainly in inventory database construction), while the environmental impact assessment methods are different in the downstream. So the overall coupling analysis method is not formed. The current paper gives rational suggestions on the coupling development of the two systems in terms of the aggregate emergy flow table, the indicator system construction and indicator evaluation methods. In addition, it is necessary to introduce sensitivity analysis and uncertainty analysis in order to improve the reliability of assessment results. At present, the research on the coupling development of the two theories is in rapid development stage, but there are still many problems that need further exploration.