Growing research suggests that endophytic fungi deeply affect plant physiology, development, and metabolism, which has become an indispensable subject in plant research. However, the micromolecular mechanisms remain vague due to the complexity of the interactions. This article summarizes the latest progress in the mechanism studies of the symbiotic relationships between endophytic fungi and plants. We address the aspects from signal generation, plant defense, to fungal coping strategies to establish the balanced constraint relationships between fungi and their hosts that finally form "a community of shared future." These processes do not occur in isolation but in synergy. Both endophytic fungi and their host plants contribute to establishing the stable symbiosis. New insights have been provided into a deeper understanding of the occurrence of species interactions and their applications to solving practical problems.
