Spatial structure analysis is beneficial to guide soil nutrients management. This paper developed a method for spatial structure of soil nutrients and analyzed these change characteristics from 2000 to 2007 using geographic information system (GIS) technology for Daxing district of Beijing, China. The results of spatial structure were obtained and occupied space proportions of total kjeldahl nitrogen (TN), alkali-hydrolyzable nitrogen (AN), organic matter (OM), available phosphorus (AP) and available potassium (AK) were 0.33, 0.22, 0.25, 0.03, 0.16 for 2000 and 0.32, 0.25, 0.23, 0.03, 0.17 for 2007, respectively. The change characteristics and influence factors for spatial structure of soil nutrients were systematically analyzed. Increased soil nutrients were exhibited three belts on the whole, whereas decreased soil nutrients were located in other regions. Natural factors and human activities drove these changes of soil nutrients. This study provides a reference for future related research.