Prefrontal cortex (PFC) is the high-level center of brain cognitive function, which regulates emotion, memory, decision-making, behavior, neuroendocrine and other brain functions. The sculpting of neural circuits during PFC development involves cellular and molecular reconfiguration. Here, we integrated analysis of single-cell transcriptome, spatial transcriptome and connectome data to decipher the spatial construction and molecular basis of neural circuits in the developing mouse prefrontal cortex.