Objective To determine the expression of carboxylic acid-terminal truncated hepatitis B virus X protein (Ct-HBx) in hepatocellular carcinoma (HCC) tissues and corresponding adjacent non-tumor tissues, and to explore its effect on postoperative prognosis of HCC patients. Methods Immunohistochemistry was performed to measure the expression levels of Ct-HBx in 462 HCC tissues, 263 matched adjacent tissues and 25 matched tumor thrombus tissues. The relationships between Ct-HBx expression and clinicopathological data and postoperative prognosis of HCC patients was analyzed. Results The positive rates of Ct-HBx in 263 HCC and paired adjacent tissues were 43.73% (115/263) and 11.79% (31/263), respectively. Multivariate Cox regression analysis showed that age, portal vein cancer thrombus (PVTT), preoperative aspartate aminotransferase (AST), preoperative α-fetoprotein (AFP), small daughter nodule, preoperative Barcelona Clinic Liver Cancer (BCLC) stage and postoperative antiviral treatment were independent risk factors of postoperative recurrence of HCC patients (all P<0.05), and the PVTT, preoperative AFP, tumor encapsulation, preoperative BCLC stage and Ct-HBx protein expression were independent risk factors for postoperative survival of HCC patients (all P<0.05). Analysis results of 263 paired HCC and adjacent tissues showed that the expression of Ct-HBx in the HCC tissues was related to gender, carbohydrate antigen 19-9 (CA19-9) and postoperative antiviral treatment (all P<0.05). Compared with the patients with negative Ct-HBx in HCC tissues and positive Ct-HBx in adjacent tissues, the patients with negative Ct-HBx in both HCC and adjacent no-tumor tissues had significantly higher 3-year disease free survival rate (P=0.050 1). Conclusion For HCC patients with negative expression of Ct-HBx in HCC tissues, the expression level of Ct-HBx in corresponding adjacent no-tumor tissues is related to the postoperative prognosis of HCC patients, and it may be a potential molecular biomarker to predict postoperative survival and recurrence.