Gastrodin (GA), p-hydroxylbenzaldehyde (HBA), p-hydroxybenzyl alcohol (gastrodigenin, HA) and parishin not only are the major active ingredients of Rhizoma gastrodiae, but exist transformed relations from each other throughout the fermentation process of Grifola frondosa in this work. We had found that parishin (non-free gastrodin) almost could completely transformed into gastrodin (GA, free gastrodin) after R. gastrodiae alcohol extract was sterilized by moist heat (121 °C, 30 min), but before was added into submerged cultivation of G. frondosa. However, interestingly and importantly, gastrodin re-synthesized of parishin after R. gastrodiae alcohol extract's addition into submerged cultivation of G. frondosa. In addition, the reduction of p-hydroxylbenzaldehyde and p-hydroxybenzyl alcohol in G. frondosa fermentation process reconfirmed that the G. frondosa strain 51616 really could synthesize gastrodin into parishin by submerged fermentation. This paper firstly also reported G. frondosa's effects on R. gastrodiae.