The cognitive and behavioral development of children and adolescents is closely related to the maturation of brain morphology. Although the trajectory of brain development has been depicted in detail, the underlying biological mechanism of normal cortical morphological development in childhood and adolescence remains unclear. By combining the Allen Human Brain Atlas dataset with two single‐site magnetic resonance imaging data including 427 and 733 subjects from China and the United States, respectively, we performed partial least squares regression and enrichment analysis to explore the relationship between the gene transcriptional expression and the development of cortical thickness in childhood and adolescence. We found that the spatial model of normal cortical thinning during childhood and adolescence is associated with genes expressed predominantly in astrocytes, microglia, excitatory and inhibitory neurons. Top cortical development‐related genes are enriched for energy‐related and DNA‐related terms and are associated with psychological and cognitive disorders. Interestingly, there is a great deal of similarity between the findings derived from the two single‐site datasets. This fills the gap between early cortical development and transcriptomes, which promotes an integrative understanding of the potential biological neural mechanisms. The underlying biological mechanism of early cortical morphological development remains unclear. We found linear development pattern of cortical thickness during childhood and adolescence is associated with spatially varying gene transcription, which expresses predominantly in astrocytes, microglia, excitatory and inhibitory neurons, and ontologically enriches for energy‐related and DNA‐related terms. Cortical development‐related genes are also associated with psychological and cognitive disorders.