With the rapid development of China's marine economy, the exploitation of uninhabited islands has received the increased attention. At the moment, governments and businesses frequently overexploit the uninhabited islands, resulting in serious damage to the island's resources and environment. The uninhabited islands' unique ecosystem and geographical location contribute to their high restoration costs following damage. The protection and exploitation of uninhabited islands drew the attention of academic world both domestically and internationally. This article establishes an ecological damage assessment model (EDAM) for the development of uninhabited islands based on the theory of island ecosystem service value (IESV). From the perspective of land-sea coordination, the EDAM fully considers different development behaviors that might disturb marine and terrestrial ecosystems on uninhabited islands. The EDAM is suitable for the pre-assessment of the development behaviors of uninhabited islands. Dayangyu island, China's first public auction of use rights, is used to demonstrate the model's scientific validity and feasibility. Additionally, the paper calculates the cost of ecological damage to the uninhabited islands using the adjusted collection standard of fund in 2018 and compares it to the cost of uninhabited islands exploitation damage compensation calculated in this paper. The findings indicate that:(1) the ecological damage compensation for Dayangyu island exploitation is 16.45 million yuan. Among them, the ecological damage compensation required for land exploitation is 8.90 million yuan, which is greater than the ecological damage compensation required for marine exploitation; (2) the land ecological damage compensation calculated in this paper has a highly ecological damage cost of 3.72 million yuan. In 2018, there was still room to increase the collection standard for tourism island use. Although the collection standard of uninhabited island use fee in 2018 includes the cost of ecological damage, the ecological damage cost in the collection standard of uninhabited island use fee fails to fully reflect the impact of exploitation on the terrestrial ecosystem. At present, the implementation of the ecological damage compensation system for the development of uninhabited islands is not only feasible in theory, but also necessary in practice. An effective assessment of ecological damages caused by uninhabited island exploitation is the foundation of a system of island ecological damage compensation that requires the damaging party to bear the cost. With a compensation system in place, it will force both governments and enterprises to carefully weigh the benefits and costs of uninhabited island exploitation so as to avoid excessive and rash development of island resources.