With the aid of the Farmland Resources Management Information System of Yongji City, the traditional geo-statistics, semivariance function, and the GS+ software, characteristics of spatial variation of 6 trace elements in the farmland soil in Yongji City were studied. Results show that among the 6 trace elements, Zn and Mo are medium in variation intensity; Fe, Mn and B, medium on the low side and Cu medium only in flood land, but medium on the low side in soils under other landforms. Cu, Zn, and Mo in blood land, Zn, B and Mo in basins, Zn and Mo on hills and Zn and Mo on mountain are all medium, but medium on the low side in soils under other landforms. In the hill area, the total spatial variation of the 6 trace elements does not only show impact of natural causes, but also those of human activities or random factors, whereas in the flood area, it does a strong spatial relativity, indicating that natural cause is the leading factor. The research on the statistical characters and the semi-variance structure of the 6 trace elements can provide land use programming with scientific basis and, overall management of soil nutrients, soil amelioration and cultivation with guidelines.