The Analytical Hierarchy Process (AHP) is a common method for systematic analysis and designing. However, when it is used in comprehensive evaluation of the ecological environment of Qinghai-Tibet Plateau, the weight of factors must be positive, and this affects the expression effect. This paper deals with the optimization of AHP in its application to this field, which improves the assignment means in the building of judgment matrix, and introduces negative numbers to the process of evaluation. Tests prove that accurate evaluation of the ecological environment of Qinghai-Tibet Plateau can be achieved by using the optimized method.