<p><i>Gastrodia elata</i> Bl. is an important medicinal orchid, but comparisons among cultivated forms can be confounded by provenance, accession background, plot microenvironment, and sample selection. We analyzed 28 selected mature tuber samples, one from each source accession, representing the red form (H, <i>n</i> = 13), green form (L, <i>n</i> = 6), and black form (W, <i>n</i> = 9) collected from Guizhou. The same 28 samples were used for 30 phenotypic and quality-related traits and terminal-bud RNA-seq, and a deliberately selected 9-sample subset was used for widely targeted metabolomics using terminal-bud tissue and exploratory transcriptome-metabolome co-variation analysis. RNA-seq included three technical replicate libraries per selected sample, and metabolomics included six technical replicate measurements per selected matched sample; technical replicates were not treated as independent biological replicates. Sixteen traits differed among selected form groups after FDR correction. Red-form samples tended to have higher gastrodin and Parishin A-C contents, black-form samples higher polysaccharide content and dry matter ratio, and green-form samples higher Parishin E and selected mineral elements. Co-expression analysis identified candidate modules correlated with medicinal constituents and processing-related traits, and the 9-sample omics subset was used only for candidate prioritization. Because one selected tuber per accession was used and key sources of variation could not be separated, the results should be interpreted as descriptive patterns in this selected sample set rather than evidence for stable form-level effects or a direct mechanistic explanation.</p>