Rumex gmelinii Turcz. (RGT) is a medicinal plant of Rumex in Polygonaceae. Our research group isolated an endophytic fungus plectosaphaerella cucumerina (Strain J-G) from RGT, which could promote the growth of the host significantly when was co-cultured with the host. In this study, we mainly used transcriptomic analysis to explore the molecular mechanism of the growth promoting effect. It was found that during the process of co-culture with Strain J-G, metabolism of amino acids, the synthesis and metabolism of carbohydrates in RGT tissue culture seedlings were all promoted, which provided sufficient material and energy basis for the growth of plants. In addition, response to hormones such as auxin and cytokinin in RGT tissue culture seedlings was improved significantly, which promoted the growth and development of plants. The repairing ability of DNA in RGT tissue culture seedlings was also enhanced to provide a good guarantee for the growth of plants. Meanwhile, defense system of RGT tissue culture seedlings was also mobilized by the existence of Strain J-G, therefore more secondary metabolites and stress resistant substances were produced to ensure the normal growth and metabolism of plants.