To explore the application of quantitative susceptibility mapping (QSM) of brain iron content in children with autism. For the control group, 40 normal children aged 2-3, 3-4, 4-5, and 5-6years were prospectively selected from June 2018 to December 2018, with equal numbers of males and females in each age group. For the study group, 40 children with autism aged 2-3, 3-4, 4-5, and 5-6years were prospectively selected from January 2019 to October 2019; once again, there were equal numbers of males and females in each age group. All children received routine head MRI scans and enhanced T2*-weighted angiography (ESWAN) sequence scans, and the ESWAN sequence images were processed by software to obtain magnetic susceptibility maps. The regions of interest (ROIs) of the frontal white matter, frontal gray matter, thalamus, red nucleus, substantia nigra, dentate nucleus, globus pallidus, putamen nucleus, caudate nucleus, pons, and splenium of the corpus callosum were selected, and the magnetic susceptibility values were measured. The differences in magnetic susceptibility between the two groups were compared in children at the same age. For the children aged 2-3years, the magnetic susceptibility values in the caudate nucleus, dentate nucleus, and splenium of the corpus callosum in the study group were lower than those in the control group (p < 0.05). For the children aged 3-4, 4-5, and 5-6years, the magnetic susceptibility values in the frontal white matter, caudate nucleus, red nucleus, substantia nigra, dentate nucleus, and splenium of the corpus callosum in the study group were lower than those in the control group (p < 0.05). The brain iron content of children with autism is lower than that of normal children. This study protocol was registered at the Chinese clinical trial registry (registration number: ChiCTR2000029699; http://www.chictr.org.cn/searchprojen.aspx ). • In this study, the brain iron content of normal children and children with autism was compared to identify the differences, which provided a new objective basis for the early diagnosis of children with autism. • This study examined the iron content values in various brain regions of normal children aged 2-6years in this region and established a reference range for iron content in various brain regions of normal children in one geographical area, providing a reliable and objective standard for the diagnosis and treatment of some brain diseases in children. • The results of this study indicate that the brain iron content of preschool children with autism is lower than that of normal preschool children.