Through pot experiment of wheat // faba bean root nylon separation(MB)，wheat // faba bean root plastic separation(PB)，wheat // faba bean root no separation(NB)，the root morphological characteristics of wheat and faba bean were systematically explored under different nitrogen application levels and intercropping conditions to provide a basis for further exploring the mechanism of crop yield in the intercropping system.The results showed that the yield of wheat，the diameter and surface area of faba bean root were all increased with the increase of nitrogen application rate.Under deficient nitrogen(N/2) condition，compared with PB and MB，the wheat root length of NB were increased by 0.66% and 2.61%，root surface area of wheat were increased by 56.14% and 52.75%，and specific root length of wheat were increased by 18.55% and 64.92%，specific root surface area of wheat were increased by 64.04% and 82.98%，respectively；the faba bean yield of NB were increased by 26.29% and 34.84%，root dry weight were increased by 35.1% and 45.4%，root surface area of faba bean were increased by 72.66% and 29.12%，root diameter of faba bean were increased by 66.67% and 14.82%，root volume of faba bean were increased by 9.55% and 5.91%，specific root surface area of faba bean were increased by 165.62% and 134.76%，respectively. The yield of wheat was positively correlated with root length and root surface area，while the yield of faba bean was negatively correlated with root length and positively correlated with specific root surface area. In different intercropping system，root morphological changes between crops were the surface driving factors affecting yield changes.Under low nitrogen environment，the higher the degree of root intercropping，the more obvious the effect.