Plant roots influence soil infiltration sources by changing pore size, distribution, and connectivity, thereby playing a crucial role in regulating the soil hydrological cycle. The extent to which root systems and soil pore structures influence the sources of soil water infiltration remains largely unclear. In this study, we investigated the three-dimensional characteristics of root and pore structure, as well as the infiltration sources, in typical forest stands (Moso bamboo and Chinese fir) using X-ray computed tomography, pore network modeling, and stable isotope techniques. The influence mechanisms of root architecture on the conversion dynamics between "new water" and "old water" during soil infiltration were quantified through the XGBoost-SHAP algorithm in combination with structural equation modeling. The results showed that (1) Significant differences in infiltration sources were observed among stand types and soil layers. The surface layer (0–10 cm) was predominantly influenced by "new water", whereas the sub-surface (10–20 cm) and deeper layers (20–30 cm) exhibited a mixture of "new" and pre-existing "old water". (2) The distinctive horizontal expansion of Moso bamboo roots led to the predominance of "new water" (16.27 mm) within the 0–10 cm soil layer, accounting for 68.02% of the total "new water" volume. In contrast, the "new water" in the Chinese fir stand (27.47 mm) was mainly distributed throughout the 0–30 cm soil profile, representing 91.11% of the total "new water" content. (3) Plant roots influence infiltration sources by altering the soil pore structure. Connected porosity and throat radius govern the transformation contributions of "new water" and "old water". These findings advance understanding of root–soil pore–infiltration interactions, providing a theoretical basis for forest water resource management.