Infantile anaemia has been a severe public health problem in China for decades. However, it is unclear whether there are regional differences in the prevalence of anaemia. In this study, we used data from the China Nutrition and Health Surveillance (CNHS) to assess the prevalence of anaemia and the risk factors associated with its prevalence in different regions. We included 9596 infants aged 0–23 months from the CNHS 2013 database. An infant was diagnosed with anaemia if he/she had a haemoglobin concentration of <110 g/L. We used multivariate logistic regression to investigate the potential risk factors associated with the development of anaemia. We found that anaemia was present in 2126 (22.15%) of the infants assessed. Approximately 95% of these cases were classified as mild anaemia. Based on the guidelines laid out by the World Health Organization, 5.5% and 43.6% of the surveillance sites were categorized as having severe and moderate epidemic levels of anaemia, respectively. The prevalence of infantile anaemia in Eastern, Central and Western China was 16.67%, 22.25% and 27.44%, respectively. Premature birth, low birth weight, breastfeeding and residence in Western China were significantly associated with higher odds of developing anaemia. Female sex and having mothers with high levels of education and maternal birth age >25 years were associated with lower odds of developing anaemia. In conclusion, we observed significant regional disparities in the prevalence of infantile anaemia in China. Western China had the highest prevalence of infantile anaemia, and rural regions showed a higher prevalence of anaemia than urban regions.