Intercropping is considered an effective practice to improve farmland productivity and root plasticity is a major reason for the high yields from intercropping. Understanding the changes in root systems is crucial for optimizing intercropping systems. Previous investigations of intercropping root systems have focused mainly on the impact of interspecific interactions on root distributions, with relatively less attention paid to the allocation of assimilates in root systems and the morphological characteristics of roots in the maize/soybean intercropping system, especially under different water and nitrogen (N) conditions. In this study, a two-year field (2022-2023) experiment was conducted in the eastern hilly area of the Loess Plateau in a two-factor split-plot design, with three cropping patterns (sole maize, sole soybean, and maize/soybean intercropping) as the main treatments, and N fertilizer application (no N fertilizer and N fertilizer) as the sub-treatments, to quantify the effects of nitrogen application on the root plasticity of the maize/soybean intercropping system between years of different rainfall. The results showed that maize/soybean intercropping enhanced land use efficiency, with a land equivalent ratio (LER) of 1.09-1.16. Compared with sole cropping, the yield per unit area of intercropping maize increased by 21.3 %-29.3 %, but that of intercropping soybean decreased by 7.7 %-14.2 %. Intercropping changed the allocation of assimilates in both maize and soybean, such that the root:shoot ratio of intercropping maize decreased by 4.5 %-17.8 %, and that of intercropping soybean increased by 27.8 %-41.5 %. In the wet year, intercropping maize and soybean exhibited a shallow root growth pattern, whereas maize demonstrated a deep root growth pattern during the dry year. The roots of intercropping maize tended to grow towards the border rows of intercropping soybean, where the root length density (RLD) of soybean decreased by 36.6 %-49.5 %. In addition, differing moisture and N conditions altered the root morphology of maize and soybean, with N application and intercropping increasing the proportion of thick roots in maize and soybean in the upper soil layer in 2023. In summary, across different water and nitrogen conditions, the plasticity shown by maize and soybean in the allocation of assimilates, root distribution, and root morphology promoted an increase in yield in the intercropping system. Our research results help researchers to better understand the mechanisms of root interactions in the maize/soybean intercropping system, facilitating a more reasonable arrangement of intercropping planting patterns.