Prenatal hypoxia is a major environmental risk factor for neurodevelopmental disorders, yet effective prenatal therapeutic strategies remain lacking. This study aimed to develop a transferrin-modified lipid nanoparticle platform for targeted delivery of HIF-1 siRNA to the fetal brain and to evaluate its therapeutic efficacy and molecular mechanisms. Transferrin-modified lipid nanoparticles encapsulating HIF-1 siRNA were intravenously administered to pregnant rats prior to hypoxic exposure. Biodistribution, gene silencing efficiency, molecular signaling alterations, neuronal structural changes, and behavioral outcomes in offspring were systematically assessed. In this study, we developed a transferrin-modified lipid nanoparticle system for non-invasive, transplacental delivery of HIF-1 small interfering RNA to the fetal brain, achieving a siRNA encapsulation efficiency of 84.18% and a loading capacity of 2.5%. Systemic administration to pregnant rats prior to hypoxic exposure resulted in preferential accumulation of nanoparticles in fetal brain tissue and effective suppression of HIF-1 expression in the fetal hippocampus without overt effects on offspring survival, as evidenced by comparable offspring survival rates across all groups (p > 0.05). Prenatal hypoxia induced sustained elevation of HIF-1 protein (p < 0.001), impaired phosphatase and tensin homolog (PTEN) activity through increased phosphorylation (p < 0.01), aberrant activation of the PI3K/AKT signaling pathway (p < 0.05), and deficits in hippocampal neuronal structural plasticity, including reduced dendritic spine density (p < 0.0001) and dendritic complexity (p < 0.0001), accompanied by autism-like behaviors in offspring, including impaired social preference (p < 0.01), prolonged self-grooming (p < 0.0001), and increased marble-burying (p < 0.001). Prenatal HIF-1 silencing restored PTEN functional status, normalized PI3K/AKT signaling, improved dendritic architecture to levels comparable to controls (p > 0.05 vs control), and significantly ameliorated behavioral abnormalities (social preference and stereotyped behaviors, p < 0.0001). Mechanistic analyses revealed that although HIF-1 binds to the PTEN promoter (ChIP-qPCR, p < 0.01), prenatal hypoxia did not alter PTEN transcript or total protein levels (p > 0.05), indicating that HIF-1 primarily regulates PTEN function at the post-transcriptional level in vivo. These findings identify a HIF-1 /PTEN/PI3K/AKT signaling axis as a key molecular pathway underlying hypoxia-associated neurodevelopmental impairment and demonstrate the feasibility of targeted prenatal gene modulation using transferrin-modified lipid nanoparticles. This work provides a nanomedicine-based framework linking environmental risk factors to early-life preventive strategies for neurodevelopmental disorders.