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Head and neck squamous cell carcinoma (HNSCC) remains a leading cause of cancer mortality worldwide, with treatment resistance posing a major clinical challenge. The tumor microenvironment, particularly the three-dimensional (3D) extracellular matrix architecture, plays a critical role in driving therapy resistance, yet the underlying molecular mechanisms remain incompletely understood. Here we investigate how the 3D collagen microenvironment orchestrates chemoresistance through NF-κB/STAT3 signaling and partial epithelial-mesenchymal transition (EMT) in HNSCC. Using 3D type I collagen culture systems, both FaDu and CAL27 HNSCC cells form spheroidal structures with cytoskeletal reorganization. Compared to 2D monolayers, 3D collagen culture activated NF-κB signaling, upregulated stemness marker ALDH1A1 and drug resistance proteins ABCG2/Bcl2, and significantly increased IC50 values for paclitaxel and cisplatin in FaDu and CAL27 cells. NF-κB inhibitor PDTC reversed these phenotypes, reducing resistance marker expression and restoring chemosensitivity. In FaDu xenografts, PDTC combined with paclitaxel exerted enhanced antitumor effects, achieving greatest tumor growth inhibition. Mechanistically, we identified a signaling hierarchy with NF-κB upstream of STAT3; PDTC suppressed both pathways, while Stat3 inhibitor Stattic only affected STAT3 downstream effectors. Clinical relevance was confirmed by immunohistochemistry of human HNSCC specimens, showing spatial enrichment of p65/p-p65 at the tumor-stroma interface specifically in lymph node-positive cases, with p-p65 H-scores significantly higher in metastatic patients (p < 0.05). Importantly, 3D collagen induced a partial EMT state with concurrent E-cadherin and N-cadherin upregulation, downregulation of ZO-1 and upregulation of Slug. Using a 14-gene p-EMT score in chemoresistant patient data, RELA and STAT3 strongly correlated with this hybrid score (RELA: R = 0.75; STAT3: R = 0.82) and activated mesenchymal genes while preserving epithelial identity. These findings demonstrate that the 3D collagen microenvironment activates an NF-κB-Stat3 signaling axis that drives cancer stemness, p-EMT, and chemoresistance in HNSCC, highlighting NF-κB inhibition as a promising therapeutic strategy to overcome microenvironment-mediated resistance.