Objective To investigate the statuses of hepatitis B virus (HBV) prevalence and hepatitis B vaccination coverage in children of the migrant workers, so as to provide the evidence for HBV control and prevention in Shanghai. Methods An epidemiological survey was conducted with 1 071 children of the migrant workers; the children were from the kindergartens, primary and secondary schools in five urban-rural fringe communities in Pudong New Area of Shanghai. Fasting bloods samples were collected to detect the biomarkers and DNA titer of HBV. Results The hepatitis B vaccination coverage rate was 87.1% (933/1 071); the coverage rate of students under the age of ten was significantly higher than those at 10 years of age or older (P<0.01); the coverage rate in children of the Han nationality was significantly higher than that of the other minorities (P<0.001), and the coverage rate in children whose parents with the college education background and above was higher than that of children whose parents with a lower education background (P<0.001). The positive rate of HBsAg was 0.7% (7/1 071) in this study. We found that age and HBV infected relatives in the family were the main risk factors of HBV infection in children (P<0.05). The positive rate of HBcAb was 1.7% (18/1 071) in the present study, which was positively correlated with the age of children (P<0.01). The positive rate of HBsAb was 33.9% (363/1 071), and the rate decreased with the age increase between 3 to 14 years old and increased with the age increase after 15 years old (P<0.001). The positive rate of HBsAb was significantly higher in other minorities than that in the Han nationality (P<0.001). The proportion of children with low level of HBsAb titer decreased with the increase of age, while the proportion of children with normal and high level of HBsAb increased with the increase of age (P<0.01). Conclusion The hepatitis B vaccination coverage rate in the children of migrant workers is lower than that in the local children of permanent residents. The positive rates of HBsAg and HBcAb witness a great decrease compared with those in 2006. More efforts should be made to strengthen the hepatitis B vaccination for the children of migrant workers.