The implementation of value assessments and analysis of the effectiveness of protection of different types of threatened and endangered species has become a key issue in biodiversity research. Current research into threatened and endangered species focuses on defining the level of endangerment and determining the priority of protection, and it is subject to problems, such as cross-management of different protection levels, lack of value assessment methods, and repetitive calculations. In this study, the number of different endangered species in Xiamen was determined using the IUCN endangered grade and the list of endemic species in China. Based on this, the emergy/GDP ratio was used to estimate the number of threatened and endangered species in Xiamen City. According to the collected, summarized, and analyzed results, there are 1444 terrestrial wildlife species in Xiamen, of which 318 are threatened or endangered. The estimated emergy value of those species was found to be approximately 3.53×10¹¹ yuan in 2015 and about 3.08×10¹¹ yuan in 2010. The emergy value of threatened and endangered species in the two periods accounted for 88.31% of the total value of the species. The endemic species hierarchy in China contributed 73.25% of the emergy value, but the contribution rate of the IUCN endangerment classification was 23.24%. Research indicates that the emergy assessment method can highlight the value of threatened and endangered species in an objective manner. These results can provide technical support for decision-making in biodiversity and species conservation management.