Chromosome 22q11.21 copy number variant (CNV) is a vital risk factor that can be a genetic predisposition to neurodevelopmental disorders (NDD). As 22q11.21 CNV affects multiple genes, causal disease genes and mechanisms affected are still poorly understood. Thus, we aimed to identify the most impactful 22q11.21 CNV genes and the potential impacted human brain regions, developmental stages, and signaling pathways. We constructed the spatiotemporal dynamic networks of 22q11.21 CNV genes using the brain developmental transcriptome and physical protein-protein interactions. The affected brain regions, developmental stages, driver genes, and pathways were subsequently investigated via integrated bioinformatics analysis. As a result, we first identified that 22q11.21 CNV genes affect cortical area mainly during late-fetal periods. Interestingly, we observed that connections between a driver gene and its interacting partners, MECP2 and CUL3, also network hubs, only existed in the network of late-fetal period within cortical region, suggesting their functional specificity during brain development. We also confirmed the physical interaction result between DGCR8 and CUL3 by liquid chromatography-tandem mass spectrometry. As a whole, our results could suggest that the disruption of DGCR8-dependent microRNA biogenesis plays a vital role in NDD for late-fetal cortical development.