Establishing desirable cropping systems with higher fertilizer-use efficiency and lower risk of environmental pollution is a promising approach for more sustainable agriculture development. Intercropping may facilitate phosphorus (P) uptake and reduce P-fertilizer application rates. However, how root-root interactions mediate enhanced P-fertilizer-use efficiency in intercropping under field conditions remains poorly understood. Using a long-term field experiment established in 2009, where there have been three P-fertilizer application rates (0, 40, and 80 kg P ha−1) and nine cropping systems (four intercropping combinations and corresponding monocultures), we calculated aboveground biomass, grain yield, aboveground P content, P-use efficiency indicators, e.g., the apparent recovery efficiency of applied P, and diversity effects. We also investigated the P-related physiological and morphological traits of crop species and linked root traits with agronomic indicators. We found that 12 years of intercropping significantly increased productivity, shoot P content, agronomic efficiency of applied P, and the apparent recovery efficiency of applied P in all combinations compared with the weighted means of corresponding monocultures; intercropping with 40 kg P ha−1 application showed relatively high productivity, P content and P-use efficiency. The P-uptake advantage in intercropping was mainly related to the positive complementarity effect. The companion crop species (i.e. faba bean, oilseed rape, chickpea, and soybean) exhibited greater P-mobilizing capacity than sole maize. Intercropped maize exhibited greater root physiological, e.g., rhizosheath phosphatase activity and carboxylates (proxied by leaf manganese concentration), and morphological traits (e.g., specific root length) than sole maize, partly related to facilitation by efficient P-mobilizing neighbors. The greater P-use efficiency was mainly contributed by morphological traits of maize rather than traits of companion crop species. We highlight that the enhanced P-use efficiency in intercropping systems is partly mediated by belowground facilitation, and desirable intercropping systems have the potential to save P-fertilizer input and improve the sustainability of P management in agroecosystems.