Abstract: Intercropping is an effective way of enhancing efficient use of phosphorus resources through using the biological potential of crops. This study aims to explore the relative contribution of root morphological adaptations to phosphorus absorption under intercropping, and to explore how the wheat||faba bean intercropping system promotes phosphorus uptake. Wheat and faba bean were grown hydroponically under either adequate or deficient phosphorus levels. The effect of intercropping on their phosphorus uptake, growth traits, and root morphology were analyzed. The relative contribution of root traits to phosphorus uptake by wheat and faba bean were then analyzed using the aggregated boosted trees (ABT) method. Our results showed that under phosphorus deficient conditions, the uptake of phosphorus by wheat was higher in the wheat||faba bean intercropping system than in the monoculture. Conversely, phosphorus uptake by wheat under adequate phosphorus conditions was lower in the intercropping system. The uptake of phosphorus by faba bean was higher in the intercropping system than in the monoculture under both phosphorus conditions. The intercropping system led to a total phosphorus uptake that was 1.04 and 1.28 times higher than that of the corresponding monocrop system under adequate and deficient phosphorus conditions, respectively. This result indicated an advantage of intercropping over monocropping. Crop patterns and phosphorus availability resulted in significant effect in wheat height; interaction between these two factors was also observed (P < 0.05). Intercropping led to a decrease in plant height for both species. The ABT analysis suggested that root length and diameter played a major role in phosphorus uptake by wheat, accounting for 74.4% and 25.3% uptake, respectively. Root length, diameter, and surface area all appeared to account for the uptake of phosphorus by faba bean, accounting for 48.0%, 35.2%, and 16.9% uptake, respectively. To conclude, under phosphorus deficient condition, the improved phosphorus uptake by wheat in wheat||faba bean intercropping system was the result of an increase in root length and a decrease in root diameter, while the phosphorus uptake by faba bean was improved owing to an increase in root length.