Nitrogen (N) deposition, an important global change factor, plays a great role in biogeochemical cycling in the ecosystem. As an important participant in the material cycle of soil ecosystems, bacteria are sensitive to changes in the soil ecosystem and play an important role in the effect of N deposition on soil ecosystems. A pot experiment was designed with two different N application methods (SAN: soil surface spraying and LAN: leaf surface spraying) and three N application levels (5.6 g N m^-2a^-1, 15.6 g N m^-2a^-1, and 20.6 g N m^-2a^-1) to evaluate the effects of N application on soil bacterial diversity and community of Pinus massoniana Lamb. and Schima superba Gardn. et Champ. seedlings using polymerase chain reaction-denaturing gradient gel electrophoresis techniques. The results showed that the responses of soil bacteria diversity and community to N application were different between the SAN and LAN treatments and they were influenced by season. During the wet season, the soil bacterial diversity of S. superba in the LAN treatment was richer than that for the SAN treatment, which was consistent with the variation trend of the soil bacterial diversity of the P. massoniana and S. superba seedling roots during the dry season. Compared to the SAN treatment, the relative abundance of soil Acidobacteria_Gp1 of P. massoniana was significantly higher in the LAN treatment than that in the SAN treatment (P<0.05). The relative abundance of soil Alphaproteobacteria of P. massoniana was significantly lower in the LAN treatment than that in the SAN treatment for the wet season (P<0.05); however, it was not significantly different for the dry season (P>0.05). N application increased the bacterial diversity of the S. superba soil and the relative abundance of Proteobacteria in the P. massoniana soil. N application stimulated the relative abundance of soil Actinobacteria of P. massoniana; however, it decreased the relative abundance of soil Acidobacteria of S. superba. The soil bacterial community was significantly correlated with soil pH (P<0.05) and was significantly influenced by soil NH₄⁺-N content (P<0.05) in the S. superba soil.