Objective: To evaluate the safety of population based sequential vaccination schedule of inactivated poliovirus vaccines prepared with different strains. Methods: This randomized, parallel-group controlled trial was conducted from March, 2017 to May, 2018, in Shanghai. Adverse reaction data of Sabin strain inactivated polio vaccine (sIPV), wild strains inactivated polio vaccines (wIPV) and bivalent types Ⅰ and Ⅲ oral poliomyelitis vaccine (bOPV) were systematically collected through active observation in 1 917 infants in Shanghai after the vaccination at 2, 3, 4 months old. The eligible infants aged 2 months were divided into 4 groups: ①sIPV+sIPV+bOPV group; ②sIPV+wIPV+bOPV group; ③wIPV+sIPV+bOPV group; ④wIPV+wIPV+bOPV group. Results: The incidence of adverse reaction 30 days later after 3 basic dose vaccinations was 16.79% (946/5 633). No serious adverse reaction was reported. Local and systemic reactions were mainly mild. Common local reactions were pain, erythema, cutaneous nodule, etc.; and common systemic reactions were abnormal crying, drowsiness, diarrhea and appetite lost, etc.. The incidence of local reactions 30 days later after 3 basic dose vaccinations was 1.65% (93/5 633), and the incidence rates of grade 1-3 reactions were1.26% (71/5 633), 0.21% (12/5 633) and 0.20% (11/5 633) respectively. The incidence rate of systemic reactions 30 days later after 3 basic vaccinations was 15.14% (853/5 633), and the incidence rates of grade 1-3 reactions were 11.33% (638/5 633), 3.18% (179/5 633) and 0.64% (36/5 633) respectively. There were no significant differences in the rate of grade 3 reaction among different groups (χ(2)=4.17, P=0.24). Conclusions: No severe adverse reactions related to sequential vaccination of different strain inactivated polio vaccines were observed, most of reactions were mild and all of them were cured. It is safe to use sIPV and wIPV simultaneously or alternately for childhood sequential vaccination.