Childhood maltreatment (CM) is a major risk factor for numerous mental disorders. The long-term consequences of CM on brain structural and functional plasticity have been well documented. However, the neurophysiological biotypes of CM remain unclear although the childhood trauma questionnaire uses different dimensions to assess trauma types. Here, we investigated neurophysiological biotypes of CM using spectral clustering and further evaluated the neurobiological heterogeneities with multimodal magnetic resonance imaging. Moreover, we established the molecular basis for each biotype of CM using brain-wide transcriptome-neuroimaging spatial association analyses. Three neurophysiological biotypes of CM with distinct structural and functional characteristics were found. The specific structural pattern for each CM subtype was found to be associated with genes primarily mediating synapse development and neuron projection. Taken together, our findings provide the initial neurophysiological and molecular evidence that CM has different biotypes, which may facilitate early precise prevention for CM and better to links this high risk factor with different psychiatric disorders.