Abstract: Objective To investigate the status on vaccination for National Immunization Program (NIP) among migrant children in Longwan District of Wenzhou City, and to explore the factors that influenced the vaccination rate in migrant children. Methods By using PPS sampling method, a series of 366 migrant children who were born from January 1, 2009 to December 31,2011 were investigated for NIP vaccine immunization status by household visit in 30 towns. Results The percentage of migrant children with vaccination card and vaccination certificate were 92.90% and 99.73% respectively. Vaccination coverage rates were Bacillus Calmette Guerin (BCG)(98.09%), 1 Oral Poliomyelitis Attenualed Live Vaccine (OPV)(95.08%), 3 Diphtheria, Tetanus and Pertussis Combined Vaccine (DTP)(92.90%), 1 Measles Attenuated Live Vaccine (MV)(91.53%), 3 Hepatitis B Vaccine (HepB)(95.36%), 1 Japanese Encephalitis Vaccine(JEV)(65.30%), and 2 Meningococcal Polysaccharide Vaccine(MPV)(74.74%), Hepatitis A Vaccine(HepA)(61.34%). In addition, the coverage of HepB first doze timely vaccination was 88.52%,the scar rate of BCG was 96.58%. Five vaccines vaccination rate was 81.97%. The boosting vaccination rates of MCV,DTP,and JEV were 78.87%,68.04%,and 57.95% respectively. The incidence of unqualified vaccination were 1.91%-42.05%, the highest being that of HepA and the lowest BCG. Conclusion Basic immunization rates of BCG, OPV, DTP, MCB and HepB were higher than 90%, but their revaccinations and the vaccination rates of JEV, MPV and HepA were low, which was the weak link in management of migrant children. The main reasons for unqualified vaccination were extended vaccination, unvaccination or not full vaccination.