Abstract: Using a whole series of Chinese Spring-substitution lines, Chinese Spring, and the chromosome donor Synthetic 6x as the materials, effects of each chromosome from genome A, B, and D on nitrogen efficiency under deficient-N condition were elucidated. It is found that the tested chromosome substitution lines, and the donor could be classified into three group, high-N efficiency, mid-N efficiency and low-N efficiency, by using the dry mass per plant. The line 6D has the highest dry mass per plant among them. With the decline of the N efficiency in the tested lines, the plant height, leaf age, root numbers per plant, leaf area per plant, chlorophyll content, Fv/Fm and photosynthetic rate are decreased. There is a significant positive correlation between the dry mass per plant and the accumulative N amount per plant. There are significant positive correlations between leaf age, leaf area per plant, chlorophyll a content, chlorophyll b content, and photosynthetic rate, while the correlation coefficient of nitrogen content and nitrogen efficiency is low. Therefore, the capacities for tolerance of deficient-N are modified largely resulted from the single chromosome substitution in wheat, and with the variable effects from different chromosomes. The donor chromosome 6D and other chromosomes that the substitution lines classified into high-N efficiency group contain the major genes regulating high-N efficiency. The morphological traits and physiological parameters, such as leaf age, leaf area per plant, chlorophyll a content, chlorophyll b content and photosynthetic rate, could be used as the potential criteria for evaluating the nitrogen efficiency of wheat under deficient-N condition.