The self-organization mapping (SOM) neural network algorithm is a new method used to identify the ecosystem service zones at regional extent. According to the ecosystem assessment framework of Millennium Ecosystem Assessment ( MA), this paper develops an indicator system and conducts a spatial cluster analysis at the 1km by I km grid pixel scale with the SOM neural network algorithm to sort the core ecosystem services over the vertical and horizontal dimensions. A case study was carried out in Xilingol League. The ecosystem services in Xilingol League could be divided to six different ecological zones. The SOM neural network algorithm was capable of identifying the similarities among the input data automatically. The research provides both spatially and temporally valuable information targeted sustainable ecosystem management for decision-makers.