The sustainable island implicates the integrated development of ecological environment with agriculture, tourism, trade, and other industries in a long term. In this study, an emergy-based framework was built to assess the sustainability of three islands states in a time series (2000, 2005, 2010, and 2015). Compared with other regions, islands are more fragile and sensitive to environmental challenges that threaten the ecosystems. Under such circumstances, we initially focused on three typical island countries of Southeast Asia, including Indonesia, Malaysia, and the Philippines, mainly for their rich natural resources accompanying rapid economy growth and urbanization processes. Results present different features for each country. Indonesia has the largest total emergy (1.53E + 24 sej in 2015), whereas Malaysia has the highest emergy use per capita (2.07E + 16 sej/cap in 2015). Another finding is that renewable resource fractions in total emergy are all steadily declining over the investigated time, whereas Indonesia experienced the largest decreasing rate but became increasingly dependent on nonrenewable resources (N), Meanwhile, Malaysia and Philippines relied more on imported inputs (F). The results also reveal that Indonesia has a higher emergy sustainability index (ESI). But when the new indicator environmental index of sustainable development (EISD) was applied to measure sustainability. The Philippines had the highest value (0.71) in 2015, whereas Malaysia had both the lowest ESI and EISD values because of factors like frequent economic activities as well as conflicts between humans and land. Results suggest that, it is essential to improve energy efficiency by technological innovations, and the removal of subsidies to fossil fuels and the strengthening of pollution control are also suggested. The outcomes can also provide policy insights to enhance sustainability of similar island economies.