Objective To investigate the expression of pre-B-cell leukemia homeobox gene 3(PBX3) and complement C1q binding protein(C1QBP) in laryngeal cancer, and explore their relationship with clinical prognosis. Methods 132 patients with laryngeal cancer treated in our hospital from January 2018 to January 2020 were selected. Real-time fluorescence quantitative polymerase chain reaction was used to detect the expression of PBX3 and C1QBP mRNA in cancer tissues and adjacent tissues. The expression of PBX3 and C1QBP protein in tissues was detected by immunohistochemistry. Pearson correlation analysis was used to analyze the correlation between PBX3 and C1QBP mRNA expression in cancer tissues. The expressions of PBX3 and C1QBP in laryngeal cancer tissues of patients with different clinicopathological characteristics were compared. Kaplan-Meier curve was used to analyze the differences in 3-year survival rate of patients with laryngeal cancer in different PBX3 and C1QBP mRNA expression groups. COX regression analysis was used to analyze the factors affecting the prognosis of patients with laryngeal cancer.Results The relative expression levels of PBX3 and C1QBP mRNA in cancer tissues were (3.72±0.58) and (3.11±0.43), which were significantly higher than (1.12±0.27) and (0.79±0.22) in adjacent tissues, and the difference was statistically significant (t=46.692, 55.185, all P<0.001).The positive rates of PBX3 and C1QBP in CRC cancer tissues were 96.77% (60/62) and 91.94% (57/62), which were higher than 9.68% (6/62) and 12.90% (8/62) in adjacent tissues, and the differences were statistically significant (χ2=96.458, 77.633, all P<0.001).PBX3 mRNA expression was positively correlated with C1QBP mRNA expression (r=0.712, P<0.001).There were significant differences in the expression of PBX3 and C1QBP mRNA in tumor tissues of different TNM stages, tumor differentiation and lymph node metastasis (all P<0.001).The 3-year survival rates of PBX3 mRNA high expression group and low expression group were 70.77% (46/65) and 92.65% (62/67), and the 3-year survival rates of C1QBP mRNA high expression group and low expression group were 71.88% (46/64) and 91.18% (62/68). The 3-year cumulative survival rate of PBX3 and C1QBP mRNA high expression group was lower than that of PBX3 and C1QBP mRNA low expression group, and the difference was statistically significant (Log-Rank χ2=12.761, 10.910, all P<0.001).TNM stage Ⅲ～Ⅳ, lymph node metastasis, high expression of PBX3 mRNA and high expression of C1QBP mRNA were independent risk factors for poor prognosis of patients with laryngeal cancer (all P<0.001).Conclusion The expression of PBX3 and C1QBP is increased in laryngeal carcinoma, and they are related to TNM stage, tumor differentiation and lymph node metastasis, which are independent risk factors for the prognosis of laryngeal carcinoma