Endophytic fungi microbiomes are a special group, living in various tissues of plants such as roots, stems, and leaves. They can be isolated from strictly sterilized interior surface of host plant tissues on culture medium. Research have shown that bioactive secondary metabolites from endophytic fungi have unexpected medicinal potential. Moreover, there are complex interactions between endophytic fungi and their host plants, which may explain the fact that endophytes can produce plant-derived bioactive compounds. This manuscript briefly summarizes the relevant studies on bioactive compounds with biological medicinal value from endophytic fungi and the relationship with their host plant.