Evaluating the positive and negative values of ecosystem services based on different ecological units is helpful for understanding the heterogeneity of ecosystem services comprehensively and objectively. In this study, we chose Manas River Basin, a typical Mountain-Desert-Oasis system (MODS), as the study area, collected 1990, 1995, 2000, 2005, 2010 and 2015 series of Landsat remote sensing images as data sources, and used the adjusted ecosystem service value coefficient of ecosystem services to estimate the positive and negative values for different ecological units. Results revealed that:(1) From 1990 to 2015, the land use/cover of Manas River Basin changed significantly. The cultivated land, water area, and construction land showed increasing trends, whereas woodland, grassland and unused land showed decreasing trends. The cultivated land and unused land changed dramatically. The construction land increased the most while the woodland decreased the most. (2) During 1990-2015, the positive value of ecosystem services in the study area was much higher than the negative value, and the net value increased slightly. The positive value showed an increasing trend after the change of "increase-decrease-decrease-increase-increase" and the characteristic of mountain area > oasis area > desert area. Each negative value showed the increasing trend in different degrees. Of which greenhouse gases emission, fertilizer loss and water resource consumption were the most prominent negative values of ecosystem services in the basin. The sum of three negative values accounted for more than 90% of the total value of different periods. The net value of ecosystem services increased from 8947.89×10⁶ yuan at the initial stage of the study to 10409.99×10⁶ yuan at the end of the study, with an average annual increase of 0.65%. (3) The net value of ecosystem services per capita showed a declining trend, indicating more environmental pressures for the Manas River Basin.