Leguminous and nonlegume tree mixed system, as a sustainable development model for artificial forest cultivation, which plays an important role in ensuring timber yield and maintaining nitrogen balance. A pot experiment in greenhouse was conducted to investigate effects of different N fertilizer and root barriers on the seedling growth, leaf physiological, root morphology and biomass of E. urophylla and D. odorifera intercropping system. The experimental designs included three nitrogen fertilization levels of 0, 3 and 6·g N per tree and three root barrier patterns including no barrier, nylon barrier and plastic barrier. The results showed as follows: (1) seedling height and ground diameter of E. urophylla and D. odorifera presented an increasing trend with the increase of nitrogen application. Under different root barrier patterns, the seedling height of E. urophylla and ground diameter were the best without barrier, while D. odorifera grew much better under the model of the plastic barrier. (2) When compared to the non N treatment, the content of leaf superoxide dismutase (SOD) activity, peroxidase (POD) activity and soluble protein content for each species relatively increased, but the content of malonaldehyde (MDA) declined. (3) The total root length, total root surface area, total root volume, mean diameter, root tip and specific root length of E. urophylla and D. odorifera increased by applying nitrogenous fertilizers, and differed from each other significantly. Under the same nitrogen level, the root growth of E. urophylla was no barrier > nylon barrier > plastic barrier, while root growth of D. odorifera exhibited plastic barrier > no barrier > nylon barrier, and under different root barrier patterns the growth between both species was significant different. (4) The level of nitrogen, was resposible to the biomass of various organs and total biomass of E. urophylla and D. odorifera. and reached its maximum when the nitrogen level was 6 g N per plant. Among the biomass allocation of various organs, the proportion of biomass of each organ for E. urophylla was stem (40.59%) > leaf (32.37%) > root (27.04%), for D. odorifera was root (47.67%) > stem (40.08%) > leaf (12.25%). These results showed that E. urophylla and D. odorifera mixed system expanded the root horizontal and longitudinal level of nutrient ecological niche, and enlarged the space for root absorption of soil nutrients. At the same time, the root interaction enhanced the nitrogen fixation ability of D. odorifera, and it had a great impact on the production of soil available nitrogen.