The effect of fertilization methods (1 cm and 5 cm of focus methods denoted as M1 and M2,0~5 cm and 0~10 cm of soil mixed methods denoted as M3 and M4) and nitrogen fertilizer application（N 0，0.3，0.6，0.9，1.2 g/pot）on the biomass,root morphological parameters and nitrogen absorbing rice seedling were studied in order to provide information for appropriate fertilization.The results showed that the biomasses of shoot and root of N0.6 showed significant higher value compared to other treatments under the fertilizer applied in shallow soils of focus method (M1 and M2),increased by 17.8%~84.8% and 13.9%~46.9% respectively.The result of root morphological parameters showed that root morphological parameters of N0.3 and N0.6 were significantly higher than that of N1.2.The biomasses of shoot and root of N1.2 showed significant higher value compared to other treatments under the fertilizer in shallow soils of mixed method（M3 and M4）,increased by 32.6%~36.3% and 14.9%~16.2% respectively.The root morphological parameters had the increasing trend with the N application rate increase.The nitrogen absorption had same tendency with biomass.The NRE of treatment M1 was higher than M2 ,and M3 was higher than M4.Correlation analysis showed that the root morphological parameters and root nitrogen absorption had a significant relationship with the shoot biomass and nitrogen absorption.In combination with root morphological parameters and nitrogen absorbing,both the fertilizer application in shallow soils by focus method under low nitrogen fertilizer,and by mixed method under high nitrogen fertilizer were beneficial to the improvement of the rice root morphology characteristics and nutrient absorption.