Nitrogen is one of the most important limiting nutrients during tree growth. In this paper, the effects of nitrogen treatments with the exponential fertilization method, traditional fertilization method(mean fertilization) and non-fertilization on the total biomass and morphology parameters in roots of one-year-old Aquilaria malaccensis and Aquilaria sinensis seedlings were studied during a five-month period. The results suggested that N supply could significantly increase the root total biomass and root morphology parameter such as root length, root surface-area, root diameter,root volume and specific root length(P<0.05). The root total biomass and root morphology parameter of the two Aquilaria seedlings from the exponential fertilization treatment were higher than those showed from the mean fertilization treatment. The conclusion is that the plants of Aquilaria malaccensis and Aquilaria sinensis treated with exponential fertilization can reach the highest growth rate. The Lorentzian model as a multi-variable nonlinear model was firstly applied to the simulations using both base diameter and height, and performed the best fit to total root biomass in the two species with the highest correlation coefficients (R²,0.95-0.99) and smallest root mean squared deviations (RMSD,0.538-2.352) among all the examined models. The Paraboloid model accurately simulated base diameter,height, and performed the best fit to specific root length in the two species with the highest correlation coefficients (R²,0.92-0.99) and smallest root mean squared deviations (RMSD,3.218-6.692) among all the examined models.