The invention provides a method for comprehensively improving desert soil, and belongs to the field of desert soil improvement. According to the method, a selected desert area is divided into three treatment areas which are sequentially arranged in a surrounding mode, wherein the government areas respectively comprise a planting area, a sand fixing area and a protection area from inside to outside. The method for transforming the desert soil in the planting area comprises the following steps: fully mixing a high-molecular compound fertilizer with the desert soil of the surface layer of the planting area, then, irrigating the planting area, and sowing seeds and/or transplanting plants after the soil surface layer of the planting area is dried. Firstly, the desert is divided into areas according to a plan, and various measures such as desert soil improvement, sand fixing, wind prevention and the like are comprehensively used, so that sand fixing and improvement of desert in the areas canbe effectively realized, and a new idea is provided for comprehensive government and improvement of the desert.