The Eastern Sichuan Region (ESR) is one of the key pilot regions for Grain for Green Program (GGP) implementation in the upper reaches of the Yangtze River basin in China. Therefore, monitoring the effect of the GGP on the ecosystem in the ESR is important. In this study, the Mann-Kendall Trend Test Model was used to ascertain the changes in vegetation coverage. The transfer matrix was used to explore the changes in Land Use/Land Cover (LULC). LULC change direction model (LCDM) was used to preliminarily assess the impact of LULC changes on the ecosystem. The Pressure-State-Response model (PSR), reflecting the human pressure and the ecosystem state, was applied to analyze the spatial-temporal characteristics of the ecosystem health index (EHI). The time span of this study was from 1990 to 2015. The results show that the vegetation coverage changed significantly (p < 0.05), and ecosystem function developed towards positive because of the increase in the coverage of forestland and water land and decrease in the coverage of farmland. The spatial distribution of the EHI was influenced by the pattern of land use. The eastern region, associated with a large area of forestland and grassland, has a low population density and a low degree of land use exploitation, resulting in a high EHI value. The situation was completely opposite in the western region. Regarding the temporal scale, in spite of the decreasing pressure indicator, most counties had experienced an increase in the EHI. There was a clear correlation between the increased EHI values and the restored areas at the third stage (2000-2005) (p < 0.05, r2 = 0.164), but this correlation disappeared at the latter stage (2005-2015) (p > 0.05). The changes showed significant variations in time and area because of differences in the process and the intensity of the implication of the GGP.