Abstract: Objective To investigate the relationship between hepatitis B virus(HBV) genotype and their mutations on the development of hepatocellular carcinoma (HCC). Methods A cohort study on patients with chronic HBV infection was followed up. HBV genotypes were identified by nested multiplex PCR and multiplex PCR. And HBV mutations in the basic core promoter region were sequencing by PCR amplification. Results The patients infected with genotype B were followed up for an average of 8.52 years (IQR:6.67-10.75), of whom the incidence of HCC was 6.55/1 000 person-years. After follow up with an average of 8.87 years (IQR:6.85-11.33), the incidence of HCC was 11.63/1 000 person-years for the patients infected with genotype C, which were significantly higher than those infected with genotype B (P=0.006). In genotype B HBV infected patients, age (≥ 60 years), cirrhosis can increase the risk of HCC, and in genotype C patients, male, age (≥ 40 years), cirrhosis, C1653T, T1753V, A1762T/G1764A mutation as well. Interferon therapy can reduce the risk of HCC. In genotype C group, interferon treatment reduced HCC risk in patients carrying A1762T/G1764A mutation (HR=0.21, P=0.008) and in those without T1753V (HR=0.08, P=0.012) and C1653T mutation (HR=0.17, P=0.013). Conclusion HBV genotypes and mutation are closely associated with HCC. Patients infected with genotype C, carrying 1762T/G1764A mutation should be given priority of receiving antiviral treatments in order to prevent HCC; those carrying C1653T or T1753V mutation should be monitored closely to detect early HCC and receive timely surgical resection.