ABSTRACT A new vaccination schedule with one dose of inactivated polio vaccine (IPV) followed by three doses of bivalent oral attenuated live polio vaccine (bOPV) was introduced in China in 2016. Both Sabin IPV (sIPV) and Salk IPV (wIPV) sequentially with bOPV were accepted in the Chinese routine vaccination schedule. We intended to assess the immunogenicity of the current primary schedule (s/wIPV-bOPV-bOPV) and the schedule in the early stage of the switch (tOPV-bOPV-bOPV), and compare immunogenicity between the groups with different polio virus strains. Healthy infants aged 60–89 days were recruited in hospitals in Chongqing. Infants were assigned to one of three treatments (tOPV-bOPV-bOPV, sIPV-bOPV-bOPV or wIPV-bOPV-bOPV) by enrollment time. Polio neutralizing antibody (NA) assays were conducted to assess immunity. 1027 eligible infants were enrolled. Over 95% seroprotection rates against type I poliovirus (PV1) and type III poliovirus (PV3) were observed in all groups. Infants who received tOPV-bOPV-bOPV had higher antibody titers against type II poliovirus (PV2) than did the IPV-bOPV-bOPV. The geometric mean titers (GMTs) of PV2 were only ~20 in the IPV-bOPV-bOPV. GMTs of PV1 were higher than PV3 in s/wIPV-bOPV-bOPV. The primary schedule of s/wIPV-bOPV-bOPV is insufficient to protect children against PV2, and the NA titer to PV3 is lower. Higher antibody responses were induced in sIPV-bOPV-bOPV than that in wIPV-bOPV-bOPV. Supplementary vaccination with one dose of IPV is necessary for children who had no tOPV immune history or had only one IPV to induce higher levels of immunity against PV2 and PV3.