Objective To investigate the expression of methyltransferase like protein 5 (METTL5) and ubiquitin specific protease 5 (USP5) in hepatocellular carcinoma (HCC) and their clinical significance. Methods From March 2019 to March 2020, 110 patients with HCC in our hospital were collected. The expressions of METTL5 and USP5 were detected by immunohistochemistry. The relationship between METTL5, USP5 expression and clinicopathological features was analyzed. The relationship between METTL5, USP5 expression and prognosis of HCC patients were analyzed. Results The positive rates of METTL5, USP5 in HCC were 61.82% (68g110) and 63.64% (70/110), which were higher than those in adjacent tissues (7.27% (8/110) and 9.09% (10/110), and the difference was statistically significant（χ2=72.368, 70.714, P＜0.001). There was a positive correlation between METTL5 and USP5 expression in HCC tissues (r=0.718, P＜0.001). The positive rate of METTL5, USP5 in HCC with CNLC stage Ⅱ-Ⅲ and tumor maximum diameter ≥5 cm was higher than that of HCC with CNLC stage I and tumor maximum diameter＜5 cm, and the difference was statistically significant (all P＜0.05). The 3-year overall survival rate of METTL5 positive group was 36.76% (25/68), and that of METTL5 negative group was 83.33% (35/42). The 3-year cumulative survival rate of METTL5 positive group was lower than that of METTL5 negative group (log rank χ2=20.500, P＜0.001). The 3-year overall survival rate was 38.57% (27/70) in USP5 positive group and 82.50% (33/40) in negative group. The 3-year cumulative survival rate in USP5 positive group was lower than that in negative group(log rank χ2=18.690, P＜0.001). CNLC stage Ⅱ~Ⅲ, maximum tumor diameter＞5 cm, METTL5 positive, USP5 positive were the risk factors affecting the prognosis of HCC patients. Conclusion The expressions of METTL5, USP5 in HCC are significantly increased. Both of them promote the malignant progression of HCC and are potential tumor markers to evaluate the prognosis of HCC patients