Intercropping facilitates the efficient utilization of land, light, water and nutrients. It is, therefore, important to increase the biodiversity of farmland and to develop sustainable ecological agriculture in both theory and practice. Intercropping helps improve the mobilization and uptake of soil iron (Fe) and zinc (Zn) and corresponding nutritional status in the plants, thus achieving grain micronutrient biofortification. In this review, phenomena of the improvement of Fe and Zn nutrition in dicotyledonous plants as affected by intercropping with gramineous plants (e.g. maize/peanut intercropping) were summarized. Moreover, the possible mechanisms in relation to interspecific rhizosphere molecular and physiological processes, as well as the changes in interspecific root morphology and distribution and microorganisms in the rhizosphere were elucidated. The accumulation, transfer and distribution of Fe and Zn in the plants in intercropping systems were also reviewed. The possible affecting factors on nutrients of Fe and Zn were analyzed. Based on the present advances in the mobilization and acquisition of soil Fe and Zn, and their accumulation and distribution in plants as well as the related management and environment influence factors, some new research questions were pointed out. Quantitative analysis, dynamic and systemic researches and field studies on Fe and Zn transfer from soil to plant in intercropping systems should be strengthened in the future.