Objective To investigate the correlation between the expression of △Np63 and epithelial-mesenchymal transition (EMT)-related molecular markers and its clinical significance in hypopharyngeal squamous cell carcinoma (HSCC). Methods The tumor and adjacent normal epithelium tissues of 98 patients with HSCC were collected from Department of Otorhinolaryngology Head and Neck Surgery, Changhai Hospital, Second Military Medical University from Jan. 2013 to Nov. 2016. The expression of △Np63, E-cadherin and vimentin protein in HSCC tissues, adjacent normal epithelium tissues and different regions of HSCC tissues was detected by immunohistochemistry. The correlation between the expression of △Np63, E-cadherin and vimentin proteins was examined by test of Spearman's rank-correlation coefficient. The correlation between the expression of proteins and clinicopathological features was evaluated by rank sum test. Results The expression of △Np63 and vimentin in the HSCC tissues was significantly higher than that in the adjacent normal epithelium tissues (P<0.01), while the expression of E-cadherin in the HSCC tissues was significantly lower (P<0.01). Compared with the central region of HSCC tissues, the positive expression of △Np63 and E-cadherin in the border region was significantly decreased, and the positive expression of vimentin was significantly increased (P<0.05). The expression of △Np63 was positively correlated with the expression of E-cadherin (r_s=0.409, P<0.01) and was negatively correlated with the expression of vimentin (r_s=-0.333, P<0.05) in HSCC tissues. There was no significant correlation between △Np63 and T stage, lymph node metastasis, degree of pathological differentiation or other clinicopathological features. The expression of E-cadherin and vimentin was correlated with the degree of pathological differentiation and lymph node metastasis (P<0.05). Conclusion Abnormal expression of △Np63 is associated with the occurrence and development of HSCC and the expression of EMT-related markers, indicating that △Np63 may inhibit EMT in HSCC.