Objective To investigate the current situation of anaemia among children aged 6–23 months in a rural county in China, and to explore the influencing factors and the main causes of anaemia.

Design A cross-sectional study.

Setting Huzhu County in Qinghai Province, China

Participants We selected 38 sampled villages using Proportional to Population Size sampling method. We obtained the name list of children aged 6–23 months in each sampled village and planned to survey all the eligible children aged 6–23 months and their caregivers.

Primary and secondary outcomes measures The prevalence of anaemia, the influencing factors of anaemia, the laboratory tests for biological causes of anaemia, including serum ferritin, soluble transferrin receptor, folic acid, homocysteine and vitamin B12.

Results A total of 754 children aged 6–23 months and their caregivers were surveyed, and 183 anaemic children aged 12–23 months were collected venous blood sample. The anaemia prevalence of children aged 6–23 months in Huzhu County was 59.1%. Children of younger age (OR=0.968, 95% CI 0.940 to 0.998), Tibetan nationality (OR=3.123, 95% CI 1.473 to 6.623) and not introducing meat (OR=0.698, 95% CI 0.499 to 0.976) were more likely to be anaemic. More than 80% of children with anaemia were due to iron deficiency (ID), and 20.2% of them had both iron and folic acid deficiencies.

Conclusions The anaemia prevalence of children aged 6–23 months in Huzhu County was high and children of younger age, Tibetan nationality and not introducing meat were more likely to be anaemic. The main cause of anaemia was nutritional anaemia, with the vast majority being ID. Interventions of feeding counselling and nutrients supplements are appropriate and should be further strengthened.

Trial registration number ChiCTRPRC12002444.