The evaluation on the implementation effect of the ecological protection and restoration project of Mountain-Water-Forest-Cropland-Lake-Grass system is very important to ensure the project effect. In this paper, by constructing a cascade conceptual framework of "ecological disturbance change-ecosystem pattern change-ecosystem quality change-ecosystem function change-ecological effect change", and using the method of time-space comparative analysis, the ecological implementation effect of the ecological protection and restoration project in Qilian Mountain, Qinghai province was evaluated. The results showed that: (1) After the implementation of the project, the area of important ecological land has increased by 0.1%, the ecological connectivity has decreased by 0.5%, the vegetation coverage index has increased by 10.1%, and the water conservation per unit area has increased by 31.5%. It indicated that after the implementation of the project, the ecosystem pattern was relatively stable, the vegetation coverage and the dominant ecological functions have improved significantly, and the ecological interference index has increased slightly, but the overall interference intensity was small. (2) The comprehensive score of the project implementation effect is 78, which is relatively obvious in general, and the phased objectives in the implementation plan have been achieved well. These results will play a guiding role in the implementation of ecological protection and restoration project of Mountain-Water-Forest-Cropland-Lake-Grass system in Qilian mountains.