Background Decreased expression of airway epithelial-specific transcription factor NK2 homeobox 1 (NKX2-1) was associated with allergic inflammation in asthma patients. However, the expression and role of NKX2-1 in nasal polyps (NPs) with different endotypes were undefined yet. Methods We examined the expression of key cytokines (interleukin [IL]-4 IL-5, IL-13, and IL-17A, etc.) and NKX2-1 in NPs with different endotypes and control tissues by immunohistochemistry staining, qualitative polymerase chain reaction (qPCR), enzyme-linked immunosorbent assay (ELISA), and Western blot analysis. Results We found 23% of chronic rhinosinusitis (CRS) with NP (CRSwNP) patients had IL-5+ eosinophilic NPs, 40.7% of NPs were key cytokines negative NPs (KCN NPs) with less eosinophil accumulation. The expression of NKX2-1 in IL-5+ NPs was significantly lower than KCN NPs and normal controls ( p < 0.05). The expression of mucin 5AC (MUC5AC) and MUC5B, as well as goblet cells hyperplasia, were significantly elevated in IL-5+ NPs, which correlated with the decreased expression of NKX2-1 ( p < 0.05). Moreover, 'SAM pointed domain containing ETS transcription factor' (SPDEF) was significantly elevated, while expression of Forkhead Box A2 (FoxA2) was significantly decreased in IL-5+ NPs ( p < 0.05). The expression of chemokine (C-C motif) ligand 17 (CCL17) and IL-4 was significantly increased in IL-5+ NPs, which was associated with eosinophil accumulation( p < 0.05). Conclusion The downregulation of NKX2-1 in IL-5+ NPs may be associated with tissue eosinophilia and goblet cells hyperplasia. [ABSTRACT FROM AUTHOR]