The invention discloses a cotton trace irrigation, water and fertilizer integrated efficient cultivation method in arid desert areas. The method sequentially includes the steps of land selection, arrangement of a trace irrigation system, soil preparation, seed selection, seed processing, film mulching and sowing, field water and fertilizer regulation, disease and insect pest prevention, chemical regulation, and harvesting at proper time. The method is characterized in that the core of the technology is that cotton film mulching and sowing and underground trace irrigation, water and fertilizer integration make roots of cotton in a moisture and nutrient absorbing state all the time in the growth period; meanwhile, surface evaporation is reduced, water and fertilizer resources can be reasonably and efficiently utilized, and field management comprises irrigation, topdressing, disease and insect pest prevention and the like. By the adoption of the trace irrigation, water and fertilizer integrated efficient cultivation method, water and fertilizer management is carried out on underground root layers, surface evaporation is reduced, the nutrient loss is reduced, and the water and fertilizer utilization efficiency is greatly improved; compared with the prior art, the water utilization rate can be increased by 30-40%, the ecological environment is protected, the cotton yield is effectively increased, and the effects of high yield and high efficiency are achieved.