Objective To explore the mutations of hepatocellular carcinoma (HCC)-related hepatitis B virus (HBV) during mother-to-child transmission, so as to provide theoretic evidence for prophylaxis of HCC from the very beginning. Methods A total of 413 HBsAg-positive mothers and their newborns were enrolled in this study. Serum HBV DNA levels in maternal peripheral blood and cord blood of the newborns were measured using real-time quantitative PCR. Nested PCR together with cloning and sequencing methods were applied to examine the HCC-related HBV mutations in the preS and basal core promoter regions of HBV genome. All the newborns received standard HBV vaccination. Of the 413 newborns, 104 were successfully followed-up 7 months after birth, and the HBV mutations were examined if their circulating HBV DNA was detectable. Results Of the 413 newborns, 41 (9.9%) had HBV DNA level >10³ copies/mL in their cord blood. Four (3.8%) of the 104 newborns who were successfully followed up had circulating HBV DNA level >10³ copies/mL 7 months after birth. Compared to mothers without HBV trans-placental transmission, those with HBV trans-placental transmission had no increase in HBV mutations in the basal core promoter region. However, the viral mutations containing T2898G/C, C3000T, C3116T, T31C, and T52C in the preS region of HBV subgenotype C2 significantly increased the risk of HBV trans-placental transmission (P <0.05). The frequencies of the HCC-related mutations in the preS and basal core promoter regions of HBV genome were not significantly different between maternal peripheral blood and the cord blood of the newborns. Importantly, the HCC-related mutations were rarely found in the HBV-positive infants at 7 months after birth. Conclusion The HBV mutations in the preS region of HBV subgenotype C2 may affect the trans-placental transmission of HBV. However, the quasispecies of HCC-related HBV mutants have no advantage in causing chronic HBV infection in infants. The HBV mutants which can promote HCC are selected during the long term chronic infection.