Background Associated with the significant decrease in water resources, natural vegetation degradation has also led to many widespread environmental problems in the Aral Sea Basin. However, few studies have examined long-term vegetation dynamics in the Aral Sea Basin or distinguished between natural vegetation and cultivated land when calculating the fractional vegetation cover. Methods Based on the multi-temporal Moderate Resolution Imaging Spectroradiometer, this study examined the natural vegetation coverage by introducing the Linear Spectral Mixture Model to the Google Earth Engine platform, which greatly reduces the experimental time. Further, trend line analysis, Sen trend analysis, and Mann-Kendall trend test methods were employed to explore the characteristics of natural vegetation cover change in the Aral Sea Basin from 2000 to 2018. Results Analyses of the results suggest three major conclusions. First, the development of irrigated agriculture in the desert area is the main reason for the decrease in downstream water. Second, with the reduction of water, the natural vegetation coverage in the Aral Sea Basin showed an upward trend of 17.77% from 2000 to 2018. Finally, the main driving factor of vegetation cover changes in the Aral Sea Basin is the migration of cultivated land to the desert.