Prefrontal cortex (PFC) is responsible for high-level cognitive functions. However, the connectivity organization of PFC is still poorly understood. In this study, we established a highly efficient pipeline for large-scale reconstruction of whole-brain mesoscopic connectome and obtained the whole-brain projectome of over 6000 single neurons in mouse PFC, the largest database of whole-brain single-neuron projectome of mouse to date. Through comprehensive analysis, we identified 64 projectome-defined neuron subtypes in the mouse PFC and their spatial organization, the modularity and hierarchy of intra-PFC connectivity, and the correspondence between transcriptome-defined and projectome-defined neuron subtypes. The study established a comprehensive single-neuron projectome of mouse PFC, systematically studied the internal connectivity and the efferent projection patterns of PFC, and proposed a working model of the PFC, thus providing a structural basis for the neural mechanisms of high-level cognitive functions of the PFC. This work demonstrates how large-scale single-neuron projectome analysis can provide new insights into the structural principle within the brain.