Objective To investigate the status of hepatitis B virus (HBV) infection and hepatitis B vaccination in junior middle school children of migrant workers in Pudong New Area of Shanghai, so as to provide evidence for prevention and treatment of hepatitis B. Methods A total of 298 children of migrant workers were recruited from junior middle schools of five communities in Pudong New Area, where migrant workers gathered. Questionnaire survey and HBV serological test were conducted. Results The 298 students had a hepatitis B vaccination coverage rate of 70.8% (211/298) and the whole-course vaccination coverage rate of 48.3% (144/298). The vaccination coverage rate of ethnic minority students was significantly lower than that of Han students (P<0.01). The vaccination coverage rate of children whose fathers were private business owners was the highest (P<0.001). The vaccination coverage rate of children whose fathers had junior college or above education background was significantly higher than those whose fathers had a lower one (P<0.01). The positive rates of hepatitis B virus surface antigen (HBsAg) and hepatitis B virus core antibody (HBcAb) in these children were 2.3% (7/298) and 4.7% (14/298), respectively. HBV infected family member was the independent influencing factors for positive HBsAg or HBcAb (P<0.01). HBsAb positive rate was 36.6% (109/298) in these children, with that of ethnic minority students being significantly higher than that of Han students (P<0.05). The proportion of low hepatitis B virus surface antibody (HBsAb) titer (10 mU/mL≤HBsAb<100 mU/mL) in Han students was higher than that of ethnic minority students, while the proportions of normal level (100 mU/mL≤HBsAb<1 000 mU/mL) and high level (HBsAb≥1 000 mU/mL) of ethnic minority students were significantly higher than those of Han students (P<0.05). Conclusion The hepatitis B vaccination coverage rate is relatively low in junior middle school children of migrant workers, and the positive rates of HBsAg and HBcAb are slightly higher, and these children are important targets for hepatitis B prevention and treatment in Shanghai and other megacities in the future. Health management and education of hepatitis B prevention and treatment should be strengthened for migrant workers and their children.