In order to discuss the effects of nitrogen fertilizers application on the variability of paddy quality in black soil region, the example of black soil of typical cold area was taken and treated with 0, 60kg/hm2, 85kg/hm2, 110kg/hm2, 135kg/hm2 and 160kg/hm2 of nitrogen fertilizer under water saving irrigation condition. The field system sampling data for three main paddy quality indicators of protein, amylose and chalkiness in mature paddy were studied, the variability of three paddy quality indicators was investigated by using geostatistics theory, and a semi-variogram model was established. The results showed that the different nitrogen applications can not only promote paddy quality improvement, but also reduce paddy quality difference in the field area. Except that chalkiness and protein treated with no nitrogen fertilizer was the medium variation, all the other treatments were weak variation. In these three indicators, amylose was the most largest positive space correlation range, which was greater than the positive correlation of protein and chalkiness space. It was showed that the water and nitrogen management had the greatest influence on the variability of amylose in cold region. With the increase of nitrogen application rate, the nitrate nitrogen and ammonium nitrogen in soil were increased first and then decreased. The changes of nitrate and ammonium nitrogen contents in soils with different nitrogen application rates were in the opposite order to the spatial variation of paddy, which were in a descending trend as WS0, WS60, WS85, WS160, WS135 and WS110, it was showed that the different nitrogen contents had some influence on the variability of paddy quality, the results showed that the application of different nitrogen fertilizers could change the contents of nitrate and ammonium nitrogen in soil and then had a certain impact on the rice quality variability. The optimum nitrogen fertilizer application was 110kg/hm2, and the three paddy quality indexes and its growth matrix had good regional characteristics and spatial structure. The introduction of geostatistics not only compensated the deficiency of classical statistical analysis, but also provided theoretical basis for spatial structure and quantitative research of water-fertilizer-soil-crop system information.