Growth differentiation factor 6 (GDF6), a member of the TGF-β superfamily, plays multifaceted roles in tumorigenesis, yet its molecular mechanisms and cancer-type-specific regulatory networks remain poorly defined. This study investigates GDF6’s context-dependent functions through pan-cancer multi-omics integration and functional validation. Transcriptomic data from TCGA (33 cancers, n = 10,535) and GTEx were analyzed to assess GDF6 dysregulation. Co-expression networks, pathway enrichment (KEGG/GO), and epigenetic interactions (m6A, m5C, m1A) were explored. Functional assays included siRNA knockdown, wound healing, and validation in immunotherapy cohorts. GDF6 exhibited bidirectional expression patterns, with downregulation in 23 cancers (e.g., GBM, BRCA) and upregulation in 7 malignancies (e.g., KIRC, PAAD). Mechanistically, GDF6 activated the PI3K-Akt/VEGF pathways, thereby promoting angiogenesis and metastasis. It modulated epigenetic regulation through interactions with m6A readers and erasers. Additionally, GDF6 reshaped the immune microenvironment by recruiting myeloid-derived suppressor cells (MDSCs) and cancer-associated fibroblasts. Notably, GDF6’s dual role extended to immunotherapy: it suppressed anti-PD1 efficacy but enhanced anti-PD-L1 sensitivity, linked to differential MHC-II and hypoxia-response regulation. This study deciphers GDF6’s context-dependent molecular networks, revealing its dual roles in metastasis and immune evasion. These findings highlight GDF6 as a central node in TGF-β-mediated oncogenic signaling and a potential therapeutic target for precision intervention.