A questionnaire survey for parents of children under 5 years of age was conducted to analyze vaccine hesitancy with the 13-valent pneumococcal conjugate vaccine (PCV13) in Shanghai, China. A total of 892 valid questionnaires were collected. Descriptive statistical methods, Chi-square test and effect size of Cohen were used. Among participants, 421 (48.8%) had children who had been vaccinated with PCV13 before the survey while 227 (26.73%) planned vaccination with PCV13 in the future. The main reasons for not receiving vaccination were the fear of adverse reactions (79, 26.7%), beyond vaccination age (69, 23.3%), and no need to vaccinate (44, 14.9%). Reducing vaccine hesitancy and increasing vaccination willingness can be achieved through health interventions, lower vaccine prices, and the adjustment of vaccination strategies.