In order to reveal the physiological response mechanism of Fagopyrum tataricum to low nitrogen(N) stress, were conducted the pot experiment to study the effects of low N stress on the seedling growth, root physiological traits and nitrogen uptaking. The experimental materials included 2 lowN tolerant cultivars (‘Diqing kuqiao’, ‘Guangku 1’) and 2 lowN sensitive cultivars (‘Xiqiao 1’, ‘Heifeng 1’). Three results were drawn from the this experiment. (1) Compared to the normal N treatment (15 mmol/L), the plant height, stem diameter, leaf area, shoot dry weight, root diameter, root volume and root area were declined, root/shoot ratio and main root length were increased under lowN stress (0.5 mmol/L) and very lowN stress (0.05 mmol/L). Besides, the root dry weight increased to a certain stress extent under lowN stress, and the amplification of lowN tolerant cultivars was more bigger (13.69% and 19.26%); (2) LowN stress could make leaf chlorophyll content, F_m, F_v/F_m, root activity, nitrate reductase (NR) activity and soluble protein content significantly decreased, but make F_o, root superoxide dismutase (SOD) activity, peroxidase (POD) activity, malonaldehyde (MDA) content, soluble sugar content and free proline content increased; (3) Plant N content and plant N uptake significantly decreased under lowN stress, while plant N uptake efficiency increased. The study has shown that the different F. tararicum cultivars to lowN stress were significantly different. Under low N environment, lowN tolerant cultivars had the obvious advantages of growth not only because the less influence of low N pressure to agronomic character, photosynthesis and root activity, but also because the higher root protective enzyme activity, osmotic adjustment substances contents, plant N contents and plant N uptake.