Background: Human papillomavirus (HPV)-positive oral squamous cell carcinoma (OSCC) is increasing worldwide with typically higher grade and stage. Studies suggested that microRNAs (miRNAs) play a critical role in cancer; However, their role in HPV-positive OSCC progression remains unclear.Methods: miRNA microarray was performed to identify differentially expressed miRNAs. qRT-PCR and FISH were performed to determine the relative expression of miR-550a-3-5p. CCK-8, Flow cytometry, Wound healing, Cell invasion assays and xenograft experiments were conducted to analyze the biological roles of miR-550a-3-5p. Tumor-associated macrophages (TAMs) generation, co-culturing of cancer cells with TAMs, Western blot, Dual-luciferase reporter gene assay, Immunohistochemistry and animal studies were performed to explore the mechanisms underlying the functions of miR-550a-3-5p. Results: In this study, we identified 19 miRNAs differentially expressed in HPV-positive OSCC specimens. One of these, miR-550a-3-5p, was down-regulated in HPV-positive OSCC. This down-regulation correlated with higher tumor size and nodal metastasis. Biofunctional investigations revealed that miR-550a-3-5p inhibited tumor growth and progression in nude mice models without altering the in vitro migration, invasion and EMT of HPV-positive OSCC cells. After co-culturing cancer cells with tumor-associated macrophages (TAMs), we found that the effects of miR-550a-3-5p on suppressing migration, invasion and EMT of HPV-positive OSCC cells were dependent on decreasing M2 macrophages polarization. Moreover, we identified that miR-550a-3-5p, down-regulated by E6 oncoprotein, inhibited M2 macrophages polarization by YAP/CCL2 signaling, which in turn abrogating EMT program in HPV-positive OSCC cells. Using YAP inhibitor, verteporfin (VP) in a HPV-positive OSCC model of transgenic mice also showed that tumors were less progressive when compared to those in Vehicle group. In both xenografts and clinical HPV-positive OSCC samples, miR-550a-3-5p levels were inversely associated with YAP, CCL2 expressions and the number of M2 macrophages.Conclusions: E6/miR-550a-3-5p/YAP/CCL2 signaling induces M2 macrophages polarization to enhance EMT and progression, revealing a novel crosstalk between cancer cells and immune cells in HPV-positive OSCC microenvironment.