Abstract Background A nationwide investigation on the carriage proportion of H. influenzae among healthy populations is lacking in China. The purpose of the study was to review the prevalence of pharyngeal carriage of H. influenzae among healthy populations in China, and explore its influencing factors. The serotypes distribution of H. influenzae was also analyzed. Methods A systematic search was conducted with key words “Haemophilus influenzae”, “Carriage”, and “China” or “Chinese” from inception to March 2018. After careful screening, the data of included articles were extracted with a pre-designed excel form. Then, the pooled carriage proportion of H. influenzae was calculated using the random effect model. Results A total of 42 studies with 17,388 participants were included. The overall pooled carriage proportion of H. influenzae was 0.17 (95% CI: 0.13–0.21), and the carriage proportion largely varied by province. Subgroup analysis indicated that the pooled carriage proportion was 0.17 (0.13–0.21) for children, and 0.14 (0.7–0.23) for adults. There were no statistically significant heterogeneity between subgroups by age (p = 0.65), sex (p = 0.88), and season (p = 0.10). The pooled carriage proportion of Hib was 0.01 (0–0.02), while the carriage proportion of NTHi was 0.22 (0.13–0.31). Conclusion In China, the carriage proportion of H. influenzae among healthy population was low, but it largely varied by provinces.