North China is a significant ecological region with the fastest development of desertification and an extremely fragile ecology, and also seriously harmed due to the wind and sand. In this study, we consider six key national ecological function zones that are located in northern China as the study areas. We analyze the changes in the ecosystem structure and key ecosystem services such as sand fixation services, soil conservation, water conservation, and herbage allowance. Sequentially, we evaluate the effects of ecological protection, summarize the primary existing ecological problems, and provide scientific basis for decision-making on the supervision and assessment of key ecological function zones. The results indicated that except in Yinshan, the grassland area in others decreased, and the desert area of three key eastern ecological function zones increased, while that of others in the west decreased. The vegetation coverage of grassland increased from 0.4% to 7.0%. Further, the sand fixation services reduced (except in Hulunbuir); the water conservation services in Tarim river and Aerjin increased at first and then decreased, while it only increased in Yinshan and Horqin. The soil conservation services improved, while the herbage allowance decreased in all the zones. Furthermore, except in Hulunbuir and southern Hunshandak, the relationship between the herbage allowance and sand fixation was mainly synergistic, and except in the northwest of Horqin and eastern Hulunbuir, the relationship between the herbage allowance and water and soil conservation was mainly synergistic. From the changing of ecosystem and correlation analysis between the supply and regulatory services, the phenomenon of reduced grass should be controlled. The transition zone between the cropping area and nomadic area led to a relationship of tradeoff with strong contradiction between ecological protection and production. Hence, these should be key protected zones.