In this study we analyzed the existing problems of previous emergy ecological footprint model in terms of emergy density, ecological carrying capacity, ecological index classification, and integration by comparing with the existing emergy ecological footprint models, and summarized the results. Then, we established a system for estimating ecological footprint taking into consideration the consumer's perspective and supply scenario, and developed a more effective solution to improve the emergy ecological footprint and ecological carrying capacity model. Based on the improved model, the change characteristics of Hainan's ecological economic system from 2000 to 2016 were analyzed empirically. The results showed that:(1) the footprint of energy and biological products have increased dramatically, whereas pollution and construction land footprint remain stable; (2) production carrying capacity has increased owing to technological improvement, and the environmental carrying capacity has decreased owing to increased human occupation intensity and environmental resource utilization; (3) the overall ecological environment of Hainan shows ecological surplus, but pollution and energy surplus has decreased, and energy began to appear as an ecological deficit in 2011. Through the construction of footprint accounts, it is possible to track changes of the emergy ecological footprint, ecological carrying capacity, and ecological surplus/deficit of various accounts and various land types more clearly. An enhanced emergy ecological footprint model could reflect the regional ecological economic system more objectively and provide the basis for development of regional environmental management and protection.