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The inorganic nitrogen (N) that can be absorbed and utilized by plants is mainly ammonium N (NH₄⁺-N) and nitrate N (NO₃⁻-N), which may affect seedlings’ root morphology and growth through its heterogeneous distribution. Root morphology and seedling growth were investigated in a subtropical major conifer (<i>Cunninghamia lanceolata</i>) and a broadleaf tree species (<i>Schima superba</i>) under five different NH₄⁺-N to NO₃⁻-N ratios (10:0, 0:10, 7:3, 3:7, 5:5). Results: (1) While both species developed thinner roots under the treatment with a high NO₃⁻-N concentration, the roots of <i>C. lanceolata</i> were longer than those of <i>S. superba</i>. In contrast, the roots of both species were thicker under the treatment with a high NH₄⁺-N concentration, with those in <i>S. superba</i> being much longer than those in <i>C. lanceolata</i>. (2) The mixed NH₄⁺-N and NO₃⁻-N treatments were more conducive to the aboveground growth and biomass accumulation of both tree species and the underground growth of <i>S. superba</i>. N sources with high NO₃⁻-N concentrations were more suitable for underground growth in <i>C. lanceolata</i> seedlings and aboveground growth in <i>S. superba</i> seedlings. Under the N sources with high NH₄⁺-N concentrations, <i>C. lanceolata</i> tended to develop aboveground parts and <i>S. superba</i> tended to develop underground parts. (3) The roots of the two tree species adopted the expansion strategy of increasing the specific root length and reducing the root tissue density under the N sources with high NO₃⁻-N concentrations but the opposite with high NH₄⁺-N concentrations. The root-to-shoot ratio of <i>C. lanceolata</i> increased under high NO₃⁻-N concentrations, while that of <i>S. superba</i> increased under high NO₃⁻-N concentrations. These results indicate that the responses of root morphology to different N forms are species-specific. Furthermore, according to the soil’s N status, NH₄⁺-N can be appropriately applied to <i>C. lanceolata</i> and NO₃⁻-N to <i>S. superba</i> for cultivating seedlings.