Borneol is widely used in the world, but in China, as a component of traditional Chinese medicine (TCM), it has a long history. According to the difference of composition and structure, borneol can be divided into natural borneol (NB) and synthetic borneol (SB). To explore the effect of borneol toxicity on environmental health, especially on aquatic animals, 6-hour post fertilization (hpf) zebrafish embryos were exposed to 10, 30, 50, or 70 mg/L NB or SB for 96 h. Various concentrations of borneol were applied to zebrafish embryos for 96 h, and the lethal curve was obtained. The exposure of borneol caused the heart rate to slow down and yolk sac edema. After exposure to borneol, the number of macrophages and neutrophils and the development of thymus were inhibited in zebrafish larvae. The gene expression level of cxcl-c1c, il-8 and il-1β were up-regulated after borneol exposure. While the expression level of chemokines ccl1 were decreased. After exposure to NB, the gene expression level of IFN-γ showed a trend of increasing first, then decreasing and then increasing, but it always showed an upward trend in the SB exposure group. After exposure to NB, the gene expression level of rag1 decreased, but in the SB exposure group, it increased first and then decreased. Through H&E staining, we also evaluated the pathologic changes of the spleen in adult zebrafish treated with borneol and found that the spleen was injured in borneol treated group. Finally, the locomotor behavior of zebrafish larvae was decreased after NB and SB exposure. NB and SB exposure affected the expression level of neurodevelopmental-related genes (epfa4, gap43, gfap, synapsinlla) and the specific expression of related genes (krox-20, pax2) in the brain region. Therefore, our research results show that borneol has immune and neurotoxic effects on zebrafish larvae, and the toxicity of SB was higher than that of NB, which is helpful to evaluate the safety of this drug more comprehensively.