Neonatal hypoxic-ischemic encephalopathy (HIE), resulting from perinatal asphyxia-induced hypoxic-ischemic brain damage (HIBD), is a severe neurological disorder that impairs neurodevelopment, and no definitive therapies are available. The polyphenolic natural compound salvianolic acid C (SAC) exhibits antioxidant, anti-inflammatory, and antiapoptotic properties. In this study, we evaluated the efficacy of SAC in treating HIE via animal and human brain organoid experiments. Human brain organoids served as a translational platform for assessing natural product efficacy and clinical effect prediction. Rat brain tissues were harvested at two time points (24 h and 7 d after HIBD and SAC administration) for single-nucleus RNA sequencing. In vitro and in vivo experiments, including microarrays and gene silencing, were employed to confirm the sequencing findings. Our findings demonstrated that during the acute phase of HIBD, SAC suppressed signal transducer and activator of transcription 3⁺ (Stat3⁺) astrocyte-driven acute neuroinflammation, decreased inflammatory factor release, and maintained glial-immune homeostasis. During the subacute phase, SAC promoted oligodendrocyte differentiation and facilitated crosstalk between anti-inflammatory microglia and myelinating oligodendrocytes, establishing a regenerative microenvironment and enhancing neuregulin 3 (NRG3)-receptor tyrosine-protein kinase erbB-4 (ErbB4) signaling axis activity. These coordinated mechanisms highlight the dual capacity of SAC in mitigating early injury and driving structural repair in the later stages. This study revealed the pathophysiology of HIE and the multitarget neuroprotective effects of SAC against this disorder at single-cell resolution, advancing the mechanistic foundations for SAC-based therapies in neonatal brain injury.