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The Earth ecological systems offer fundamental resources and services for human social and economic development. The assessment of ecological values and services, significant for ecological and environmental protection, is mainly based on ecology and economics principles and has emphasized on the use of remote sensing and GIS technology in recent years. This paper presents a case study in which the MODIS data were used to retrieve important variables such fractional vegetation cover, net primary productivity, and so on that were incorporated into the modelling of ecological capital (EC) in Shihezi area, Xinjiang. The model for ecological capital assessment was built using the MODIS retrievals, meteorological observation, and in-situ measurements, and used to estimate the spatial distribution of the values of EC in the south Junggar border in the years from 2000 to 2009. The results indicate that the EC values of the grasslands and water bodies account for a large portion of the total in the study area. The spatial distribution of the EC is uneven, exhibiting high values in the south and low in the north of the study area. The capital values in the last ten years have been totally reduced down in the area, and the components of the capital values have varied to some extent. This was mainly caused by two reasons: climate change and human activities. The fluctuation of precipitation and rising-up temperature are main natural factors that caused the reduction and variation of regional EC values. On the other hand, the Shihezi Oasis and the surrounding areas are characterized as strong human interference in the last 50 years or so such as agricultural and urban land development, and overgrazing. The findings show that the EC has been threatened in the south Junggar border since 2000 and more restrictive policy and measures for ecological protection is necessary.