Arbuscular mycorrhizal (AM) fungi are one of the most important rhizosphere microorganisms in agro-ecosystems. It has been demonstrated that symbiosis with AM fungi can enhance the growth of host plants by improving water and nutrient absorption and increasing their tolerance ability to stress conditions. However, the positive effects of symbiosis with AM are usually being limited by the application of chemical fertilizers, pesticides, and other agronomic practices in traditional farming systems. In order to produce safe foods and maintain the balance of the natural environment, organic farming without the use of chemical fertilizers or pesticides has been practiced all over the world, and increasing attention has focused on the role of AM fungi in organic farming systems. The aim of this review was to present the advantages and enhance the application of AM fungi in organic farming systems. AM fungi influenced the physical structure of soil, alleviated environmental stress damage, increased nutrient acquisition and biomass production, and improved the quality of crop products by the external hyphae. We also discussed and analyzed the challenges of AM fungi application in organic farming systems. Based on the above, AM fungi could promote the development of organic farming in the future.