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Ninety-four percent of islands claimed by China are uninhabited. Due to the lack of protection awareness in developing and utilizing processes, many island ecosystems have suffered severe damage. The government has made measures to regulate the use of uninhabited islands and sea areas, but that is inadequate. We constructed a model of accounting for the natural resource stock and ecosystem services based on emergy analysis to incorporate the ecological cost into the current national uninhabited island use fee system. We used three uninhabited islands in Shanghai as case studies to elaborate on the valuing mechanism. The results illustrate that emergy analysis is applicable for measuring the ecological value of different ecosystems of uninhabited islands, and the price mechanism combined with the ecological capital cost fundamentally enhances the traditional use fee system within an acceptable increased price. The pricing model provides a powerful tool for sustainable use of uninhabited islands, helps policymaking, and can be extended to other uninhabited islands.