Orchids produce tiny, light seeds (dust-like seeds without endosperm) that rely on specific symbiotic fungi for successful germination. Plant roots often release small signaling molecules or bioactive compounds to attract arbuscular mycorrhizal (AM) fungi, promoting fungal growth and hyphal branching. However, until now, no such bioactive or signaling molecules have been identified in orchids that help recruit fungi for seed germination. In this study, we used metabolomics and UPLC-Q-TOF-MS/MS, combined with a molecular network approach, to explore potential bioactive/signaling molecules in the seeds of the achlorophyllous orchid Gastrodia elata Bl. Our analysis revealed the presence of amino acids, nucleotides, lipids, organic acids, saccharides, phospholipids, and lignanamides. Specifically, organic acids, saccharides, and lignanamides were shown to promote the growth of Mycena osmundicola, a fungus important for seed germination. Additionally, lignanamides inhibited the plant pathogen Fusarium oxysporum and exhibited strong antioxidant and anti-inflammatory activities. This is the first systematic identification of bioactive/signaling molecules in G. elata Bl. seeds, providing new insights into the symbiotic relationship between orchids and fungi.