Intercropping of upland rice with short-duration grain legumes has major advantages in increasing crop yields and soil productivity. However, the contribution of arbuscular mycorrhizas, the common mutualistic symbiosis between most crops and mycorrhizal fungi, is not fully understood in intercropping systems. We assayed the contribution of inoculation of the arbuscular mycorrhizal fungus (AMF) Glomus caledonium on nutrient acquisition and biomass yield. Using the method of plastic film and nylon net partition and tracing 15N transferred between the intercropped upland rice (Oryza sativa ssp. Japonica Nipponbare) and mung bean (Vigna radiata L. Chuanyuan), we compared the intercropping, with separation of the whole root systems by a plastic film, with and without a barrier of nylon net to allow penetration of the fungal hyphae. Intercropping significantly improved the formation of arbuscular mycorrhizas, particularly in the upland rice roots. The improved formation of mycorrhizas by the intercropping increased total P uptake by 57% in rice, total P and N acquisition by 65% and 64% respectively in mung bean, and nodulation by 54% in mung bean. The percentage of total 15N transfer from mung bean to rice leaves was increased from 5.4% to 15.7% by inoculation with AMF. In contrast, there was only 2.7% of 15N transfer from rice to mung bean and no AMF effect on N transfer. It is concluded that cereal and legume crop intercropping increase mycorrhiza formation, which in turn improves nodulation, N and P acquisition and N transfer in the legumes.