The study utilizes the method of Material Flow, Ecological Footprint Model and other related indicators to establish the Indicator System of Sustainable Development. Principal Component Analysis is used to abstract the representative factors in order to estimate the indicators of ecological sustainable development during 1998~2005 in Taiwan, as well as to make policy recommendations. The research indicates following results: (1) The Direct Material Input (DMI) of Taiwan shows constant instability and depends on heavy import activity. The annual increase of considerable greenhouse gas emission leads to a comparative growth of the Domestic Process Output (DOP). The both material consumption and inventory formation of the economy are unsteady. In addition, the Physical Trade Balance (PTB) indicates that supply exceeds demand, as well as the occasional shortage of building materials. (2) The 2005 per capita Ecological Demand footprint in Taiwan is 6.5392 hm2, making the Ecological Deficit per capita 4.8569 hm2. The figures reflect that productivity and life intensity of residents have exceeded the carrying capacity of Taiwan’s ecological economic system. (3) The overall Synthetic Trend Indicators of Sustainable Development in Taiwan are decreasing. Therefore, if proper measures are not adopted in time, the current weak sustainability will lead into the vicious circle which departs from sustainable development.