The Irtysh River Basin refers to a water conservation area and a vital ecological barrier in Xinjiang and also partially in Central Asia. Here, the technical solution for the ecological protection and the restoration of the Mountains-Rivers-Forests-Farmlands-Lakes-Grasslands system (MRFFLGs) pilot project in the Irtysh River Basin is refined, by complying with the core concept, i.e., “mountains, rivers, forests, farmlands, lakes and grasslands are a community of life”. The solution stresses the specific characteristics of ecologically protecting and restoring MRFFLGs in the Irtysh River Basin, which aim to reduce ecological water use, soil erosion, forest and grassland degradation, the ecological destruction of mines, water environment pollution and other issues. With overall protection, system restoration, district policy, and problem orientation as the overarching ideas, 162 sub-items of 44 major items with seven categories have been designed and implemented in the project. In addition, some highlights of the management experience that are worth promoting when the pilot project is being implemented are also summarized (e.g., the use of laws to solve historical problems, scientific argumentation and third-party evaluation, proactive guidance for the engagement of people, modern information technology support, and integration with local sustainable development). Lastly, four policy suggestions are proposed: (1) Building a model of systematic protection and restoration by using basins as the basic geographic unit; (2) Establishing and optimizing key weak links of systems and mechanisms; (3) Focusing on remedying the shortcomings of regional talents, technology and capital; and (4) Promoting the MRFFLGs project to integrate “industry, city, people, and tourism” for carrying out a large-scale system project.