Bisphenol S (BPS) is the main substitute for bisphenol A (BPA). However, the neurodevelopmental toxicity of BPS and the underlying mechanisms remain unraveled. In present study, the neuro-differentiating human embryonic stem cells, hESC, was exposed to BPS (0-375 µM) at different stages (the precursor stage, the precursor to maturation stage, and the whole differentiation stage) to assess the potential neurodevelopmental toxicity and its mechanisms. The results revealed that BPS exposure interrupted axonogenesis, manifesting a trend of initial stimulating followed by inhibition, and peaked at the intermediate dose (3.75 μM) significantly, then reached the nadir at the high dose (375 μM) significantly in the precursor to maturation stage and the whole differentiation stage. Transcriptomics analysis showed that the main interrupted pathway enriched in axonogenesis, myelination, and neurotransmitter secretion by the GO function analysis and immune-related pathway by the KEGG analysis, besides, conserved axon guidance (Slit-Robo, Netrin-DCC, Semaphorin-Plexin) and WNT signaling pathway was also enriched in KEGG pathway analysis, which previously proved to regulate axonogenesis by directly acting on growth cones and inhibit axon growth by neuroinflammatory responses. And we found that a higher neuroinflammatory response may be induced through whole-differentiation-stage exposure than the response of exposure through the precursor to maturation stage. Overall, our findings indicated the non-monotonic neurodevelopmental toxicity of BPS exposure, and the inhibition of axonogenesis was possibly mediated by conserved axon guidance and WNT signaling pathway, while neuro-immune related pathway should be further investigated.