Background: Methylmercury (MeHg), manganese ions (Mn 2+ ), and lead ions (Pb 2+ ) are ubiquitous environmental pollutants and may be neurotoxic especially during fetal development. We decided to explore the toxic mechanisms of MeHg (organic heavy metals), Mn 2+ (inorganic heavy metals) and Mn 2+ on the proliferation and differentiation of human neural stem cells (hNSCs). Materials and Methods: The proliferation and apoptosis of hNSCs were analyzed via CCK-8 method and flow cytometry under MeHg, Mn 2+ and Pb 2+ , respectively. RNA-seq was used for analyzing proliferation/differentiation mechanism of MeHg, Mn 2+ and Pb 2+ stressing hNSCs. Results: Our experiment found that when hNSCs were exposed to below 0.5 nM MeHg, 5μM Mn 2+ and 10 μM Pb 2+ , cell proliferation and differentiation were promoted. Apoptosis rates increased significantly when hNSCS were exposed to exceed 0.5 nM MeHg, 5μM Mn 2+ and 10 μM Pb 2+ . RNA-seq results showed that metal ions altered the genes expression level and signaling pathways of hNSC differentiation and proliferation, but the regulatory mechanisms of MeHg, Mn 2+ and Pb 2+ were different. Conclusion: Our findings indicated that very low-dose metal exposure may deplete hNSC pool by making prematurely differentiated neurons increase, which may be the real cause of long-term nervous system disruption in adulthood, rather than higher metal doses will cause more direct toxicity during infant development.