Arbuscular mycorrhizal fungi (AMF) have attracted significant interest in the field of sustainable agriculture. Intercropping is another sustainable practice improving the nutrient utilization efficiency. In an AMF-colonized intercropping system, intercropping has been found to increase the mycorrhization rate, including root colonization and spore population in the rhizosphere of plants. Root colonization of one plant by AMF is clearly influenced by their intercropping partners. Therefore, the selection of appropriate intercropping partners can be used to improve the activity of mycorrhizal symbiosis in crops. Furthermore, intercropping with different plant species can alter arbuscular mycorrhizal (AM) fungal diversity, and these different AM genera have distinct functions and benefits for plants in intercropping systems. Additionally, in certain intercropping systems, perennial plants serve as reservoirs of AMF inoculum for intercrops. In return, AM symbiosis enhances nutrient availability in the intercropping system, leading to positive effects of intercrops. Moreover, AMF exhibit bioprotective effects in intercropping systems, reducing the severity of plant diseases and/or compensating for plant biomass loss. However, these bioprotective effects depend on the intercropping partner rather than the degree of AM colonization. In conclusion, the combination of AMF benefits with intercropping holds great promise for improving nutrient utilization efficiency and plant health.