Using the analytic hierarchy process (AHP) in system engineering, we first establish the analytic hierarchy process (AHP) model, and take the cities that need to be established as the decision-making goal, and take the main factors that affect the ecology : forest cover rate, the number of geological disasters, water network density index, desertification land area, and air quality as the criterion layer elements. Taking the eight cities with the most serious desertification in China as the index layer, we use matlab software to run the data, and obtain the final feature vector and weight value. It is determined that Xinjiang, Gansu, and Qinghai are the areas that need to establish ecological protection zones most.