Abstract: Plant endophytes can promote plant growth and resistance to stress. They can be applied to repair damages caused by environmental pollution and protect endangered species. Certain symbiosis-related genes and microRNAs play an important role in the interactions between plants and endophytes. As a post-transcriptional regulator, microRNA associates with the regulation of plant growth and stress-resistance. This article reviews the functions of plant endophytes and the role of microRNAs plays in the plant-endophyte interactions. It is recommended future research efforts to focus not only on how and what endophytes affect plants but also the roles of plants on endophytes, as well as the non-model plants, microbial interactions, functions of microRNA in plant-endophyte interactions, and resource explorations.