Based on the data from the National Second Soil Survey, this paper analyzed the relationship between the variation of soil organic matter and the spatial scales, the variation within and among soil groups, and discussed the correlation between the soil properties and the average content of soil organic matter at various spatial-scales. The results indicated that the variation coefficient of soil organic matter content increased with increasing the number of soil profiles while individual soil profile was taken as a basic statistical unit, and decreased with spatial scale up while average of soil organic matter content in the defined scale was taken as a statistical unit. While soil taxonomy group was taken as the basic spatial unit, the variation coefficient of soil organic matter content within soil group was less than that among soil groups. The correlation between soil properties and soil organic matter content became less significant with spatial scale up. Therefore, when the grid technique or the district was applied to regionalize spatial scale, individual soil profile are needed more to reduce uncertainties of the estimate of soil organic matter in the grid or the district with spatial scale up, but the uncertainties are smaller when using soil organic matter content in well-estimate gird or district to estimate the grid or district without available data by extrapolation. When the soil taxonomy group was taken as the basic spatial scale, the result was reverse.