In response to the serious urban waterlogging and non-point source pollution, most cities in China are systematically implementing the sponge city construction, in which plants play an important role as a key ecological element. Plants could affect the soil structure, organic matter content and microbial characteristics with their root systems, and then significantly affect the water quantity and quality (nitrogen) during infiltration process, especially for ligneous plants with developed roots. In order to investigate the influence of ligneous plant roots on nitrogen during infiltration, we carried out simulation experiments on three typical ligneous plants including Sophora japonica, Malus micromalu and Malus pumila Mill. The changes of soil nitrogen and outflow nitrogen, as well as their influencing mechanisms affected by the root systems of these typical plants were investigated. The results showed that the nitrogen content in soil was positively correlated with the abundance of Chloroflexi, Proteobacteria, Gemmatimonadetes, Acidobacteria, as well as the activities of soil nitrate reductase (S-NR) and soil nitrite reductase (S-NiR). However it was negatively correlated with the abundance of Actinobacteria and the activities of soil urease (S-UE). Root system of ligneous plants mainly affect the migration of NO3—N and NH3—N by impacting the soil microorganisms and nitrogen transformation. Compared with the column without trees, the concentrations of NO3—N and NH3—N in the outflow of Sophora japonica, Malus micromalu and Malus pumila Mill. columns decreased by 30.57%, 16.58% and 15.42%, respectively; and the average contents of NO3—N and NH3—N in the soil decreased by 30.49% , 47.02% and 47.52%, respectively. The main root ligneous plants with larger root diameter and root volume contribated a higher reduction rate on the outflow nitrogen; whereas the fibrous root ligneous plants had a larger influence on the soil nitrogen content.