Regional ecological benefits can be maximized by the optimization of land use structure. In this study, the unit area equivalent factor method was used to estimate the values of ecosystem services and their changes, which were based on Landsat remote sensing image data for the Manas River Basin from 1990 to 2015. The grey structure planning model, which optimizes the land structure, was used to discuss comparisons and changes in the ecological service value (ESV) of the study area before and after optimization for maximizing ecological benefits. The results show that:(1) The grassland and unused land are the main types of land use, accounting for 70% in the basin; the area of the constructed and cultivated land is gradually increasing, whereas that of the others is slowly decreasing. (2) ESV of the river basin, decreased by 14.97% when 1990 and 2015 values were compared, showed a downward trend during the study period. The size of each individual ESV was as follows:hydrological regulation > climate regulation > soil conservation > biodiversity > gas regulation > purification environment > aesthetic landscape > food production > material production > maintaining nutrient cycle > water supply. From the perspective of spatial distribution, the value of watershed ecological services is distributed in a patch, and the division of ESV is obvious. The low mountain area has the highest ESV of about 35.84%, and climate and hydrological regulation are the main ecological service functions because the grass area is large. (3) After optimizing the configuration, the unused land area was found to be significantly reduced, whereas the other types were increased; the total ESV increased by 5.29%, and the individual values had also increased, especially hydrological and climate regulation. This study can provide a theoretical basis and practical reference for regional land-use planning and ecological civilization construction.