The ecological management of alpine permafrost area in plateau is a global problem, with few precedents for coal resource protection while ecological management. In this paper, the following results achieved in the ecological management in Muli area of Qinghai Province were understood in accordance with the idea of systematic engineering for the purpose of ecological environmental protection, with consideration to the protection of residual coal resources. Specifically, study was conducted on the ecological vulnerability of Muli mining area to damage and the difficulty of restoration under the control of natural climatic characteristics. Meanwhile, the characteristics of soil erosion and vegetation water recharge under the control of soil stratification structure were summarized. Besides, the absence and destruction of ecological geological layers was considered to be a key factor in ecological damage caused by mining. For that reason, the restoration technology of ecological geological layer was developed for the coal seam roofs and their overlying rock strata with reference to the previous achievements, an identification method of ecological geological layer was established, and the significance of ecological geological layer restoration and rehabilitation for coal conservation and ecological restoration was analyzed.