Neurovascular interactions (NVIs) are critical in establishing vascular patterning, barrier function, and in regulating cerebral blood flow, thereby maintaining neuronal homeostasis and brain health. While developmental programs and neuronal activity play a central role in cerebral cortex angiogenesis during a critical postnatal period, whether cellular heterogeneity causes region-specific angiogenic regulation remains unknown. Here, we combine spatial and endothelial single-cell RNAseq (scRNAseq) transcriptomic analysis to establish a molecular atlas of developing brain regions and a comprehensive list of spatiotemporal-specific NVIs. We find that the thalamic area has a higher vascular density than the other brain regions and our atlas identifies transforming growth factor β ( Tgfβ ) and Vegfc ligands enrichment in this area during a critical postnatal period. Neonatal endothelial Tgfβr1 deletion ( Tgfβr1iEKO ) induces vascular malformations and hemorrhages, primarily in the thalamic area. Mechanistically, we show that loss of endothelial TGFβ signaling increases VEGFC-induced AKT/mTOR signaling in vitro and in vivo , and that mTOR inhibitor Rapamycin efficiently inhibits intracerebral bleeding and vascular defects in Tgfβr1iEKO mice. Altogether, our data suggest that spatiotemporal-specific NVIs control brain vascular heterogeneity, which extends our knowledge of region-specific cerebrovascular development and will benefit our understanding of neurovascular disorders.