It is significant to analyze the spatial and temporal variation of soil nutrients for precision agriculture especially in large-scale farms. For the data size of testing results is growing every time after sampling mostly by the frequency of once a year or several months, in order to discover the variation trends of specific nutrient which would be instructive for the fertilization in the future. In this study, theories of GIS and geostatistics were used to characterize the spatial and temporal variability of soil nutrients in paddy rice fields in the Erdaohe farm of Heilongjiang Province, China, which located in the north of Daxing’an Mountains, has an area of nearly 36.1 million hectares for paddy rice planting. The soil samples, collected from 2009 to 2013 once a year, were sampled based on the spatial distribution of paddy rice fields, counting as 651 in 2009, 1488 in 2010, 954 in 2011, 483 in 2012, and 471 in 2013. These samples were analyzed for pH, soil organic matter (SOM), available nitrogen (AN), available phosphorus (AP), and available potassium (AK). In this study, we calculated and compared the spatial and temporal variation in whole farm area, using methods of exploratory statistical and geostatistical analysis. Conclusion acquired is that from 2009 to 2013, the spatio-temporal variations decreased in soil pH, AN, AP, AK, and increased in SOM. Moreover, according to the comparison of interpolation results, these five soil properties in Erdaohe farm remained not very stable in the past five years, which could implicate important significance in future research for consideration of correlation amongst fertilization, rice yield and other factors especially in large-scale farms.