In this paper, we developed a series of assessment indexes based on the evaluation of ecological effects, which consists of the ecosystem structure, qualities, services, and main impacting factors for these changes. Comprehensive monitoring and assessment methods that focused on the planning objectives of ecological conservation and restoration project were developed based on field observation, remote sensing monitoring and quantitative simulation of ecological processes. Then we assessed the ecological effects of the first- stage of ecological conservation and restoration project in Sanjiangyuan region by adopting the trend analysis of dynamics in ecosystem structure and services. The results showed that since the beginning of the project eight years ago, the macro- situation of ecosystem in this region has been getting better but not reached the best situation in the 1970s. The continued degradation trends of grassland have been initially contained, but it is difficult to achieve the expected objective of "the vegetation coverage of grassland increasing by an average of 20%-40%". The wetland and water-body ecosystems have been restored. The water conservation service of ecosystem and water supply capacity of watershed were increased, and the volume of ecosystem water conservation reached the objective of increasing by 1.32 billion m~3. The ecological restoration in the project regions tended to be better than that outside the project regions. In addition to climate change, implementation of the ecological conservation and restoration project had obvious and positive effects on vegetation restoration. However, the degradation situations of grassland were not fundamentally reversed, and the implementation of the project has not been curbing the increasing trend of soil erosion. Therefore, the local and preliminary characteristics of the first-stage of the project highlighted the long-term and arduous ecosystem conservation and protection in the Sanjiangyuan region.