In this study, the MFA and IPAT analysis methods have been used to calculate the natural material input and material output of the environmental-economic system in Hainan Province during the period from 1990 to 2005, and the results have been compared with the corresponding data of Guangdong Province. This study demonstrates that the MFA and IPAT analysis methods are good tools for evaluating the degree and discovering the mechanism of sustainable development in a region, as well as improving the quality of monitoring, controlling and decision-making of the regional development. These methods play important roles in improving the material input and output efficiency, reducing the intensity of resource-use and material output, and improving the potential of regional sustainable development. The analysis result indicates that DMI has an uprising trend with average annual increase of 6.50%, while the growth rate was moderate and RPO has a declining trend with an annual 1.25% decrease. Material input growth rate is far less than the GDP growth rate (annual average growth of 15.63%). Rapid economic growth of Hainan Province dependents on the natural resource input to a certain extent, meanwhile it also produces a certain amount of waste. The calculations of material input and output intensity and efficiency indicate that material input intensity was increased and the output intensity was decreased, while the material input efficiency and output efficiency had been gradually improved between 1990 and 2005 in Hainan Province. From the rapid economic growth and, a relatively gentle of material input and reduction of material output, we can tell that Hainan Province has initially achieved the sustainable development of the natural resource and environment. From the analysis result of material input and output of environmental-economic system, we can also see that Hainan's sustainable development is still immature. The decomposition analysis of the DMI and the RPO, shows that, from 1990 to 1997, the input of natural resources of Hainan environmental-economic system had a minimum growth, but the output had a slight increase; From 1997 to 2005, the growth rate the of natural resources input had a big increase, but the output was in decline. Obviously, the sustainable development of Hainan Province was not stable during two different phases. Therefore, the sustainable development of Hainan should be further strengthened.