Nasopharyngeal carcinoma (NPC) is prevalent in East Asia and Southeast Asia. However, the specific interactions between tumor cells and the tumor microenvironment (TME), which are implicated in poor prognosis and immune evasion, remain to be elucidated. The study incorporated single-cell sequencing data from 488,771 cells across 82 samples. Initially, single-cell RNA sequencing data (including 269,521 cells from 50 samples) and bulk RNA sequencing data (n = 183 NPC patients) with clinical features were collected to investigate the correlation between cell types and patient prognosis through scissor and scAB analysis. Our results revealed that several special cell subtypes, including Mal (TUBB2B+), Treg (TNFRSF4+), CD8_Tex (OASL+), B (EBI3+), Mϕ (ADAMDEC1+), Mϕ (CXCL10+), and pDC (TNFRSF17+), were associated with poor prognosis in NPC patients. Further analysis revealed that Mal (TUBB2B+) cells might activate Treg (TNFRSF4+) cells via the ICOSLG-ICOS pathway. Subsequently, Treg (TNFRSF4+) cells exert immune inhibitory effects on T cells, NK cells, B cells, and myeloid cells. Specifically, CellChat and spatial transcriptome analysis have revealed the activation of the CTLA4-CD80/86 pathway between Treg (TNFRSF4+) and B cells/myeloid cells, as well as the interaction of CD48-CD244A between Treg (TNFRSF4+) and NK cells. These findings were further corroborated by our single-cell RNA data and multiplex immunohistochemistry results, which provided additional substantiation for the observed interactions. These observations regarding the interaction between the tumor microenvironment and nasopharyngeal carcinoma have significant clinical implications for the future treatment of NPC.Copyright © 2025 Elsevier B.V. All rights reserved.