Gastrodia elataBlume (GE), a traditional and precious Chinese medicinal material, has been approved as a functional food. However, understandingGE’s nutritional properties and its molecular basis remains limited. Here, metabolomic and transcriptomic analyses were performed on young and mature tubers ofG. elata.f.elata(GEEyandGEEm) andG. elata.f.glauca(GEGyandGEGm). A total of 345 metabolites were detected, including 76 different amino acids and their derivatives containing all human essential amino acids (e.g., l-(+)-lysine, l-leucine), 13 vitamins (e.g., nicotinamide, thiamine), and 34 alkaloids (e.g., spermine, choline).GEGmhas higher amino acid accumulation thanGEEy,GEEmand GEGy, and vitamin contents were also slightly different in all four samples. Implying thatGE, especiallyGEGm, is a kind of excellent complementary food as amino acid nutrition provider. From assembled 21,513 transcripts (genes) based on the transcriptome, we identified many genes that encode enzymes (e.g., pfkA, bglX, tyrAa, lysA, his B, aroA), which are responsible for the biosynthesis of amino acids and enzymes (e.g., nadA, URH1, NAPRT1, punA, rsgA) that related to vitamins metabolism. A total of 16 pairs of the differentially expressed genes (DEG) and differentially accumulated metabolites (DAM) (e.g., gene-tia006709 coding GAPDH and l-(+)-arginine, and gene-tia010180 coding tyrA and l-(+)-arginine) and three DEG-DAM pairs (e.g., gene-tia015379 coding NadA and nicotinate d-ribonucleoside) show significant similar positive or negative correlation based on three, and two comparisons ofGEEy vs. GEGy,GEGy vs. GEGm, GEEyvs. GEGyandGEEm vs. GEGm, which involved into amino acid biosynthesis, and nicotinate nicotinamide metabolism, respectively. These results prove that the enzyme coded by these DEG promotes (positive correlation) or inhibits (negative correlation) the biosynthesis of parallel DAM inGE. Overall, the data and corresponding analysis in this study provide new insights into the nutritional properties ofGE and therelated molecular basis.