Objective To assess the acute organ toxicity of Strychnos nux-vomica with zebrafish model visually. Methods To assess acute toxicity, we initially determined the lethal concentration after Strychnos nux-vomica treatment for 24 h. Zebrafish was treated with five concentrations ≦ LC10 for 24 h, and the effects of Strychnos nux-vomica on morphology, function of heart, central nervous system, liver, kidney and organ-specific cell death were assessed. Next, we assessed the reversibility of toxic effect. Results Strychnos nux-vomica has an effect on the different organs of zebrafish, including heart, central nervous system, liver, and kidney, and cadiotoxicity induced by Strychnos nux-vomica was reversible to some extent. Conclusion Zebrafish model is suitable for confirming the toxic target organs for Chinese traditional medicine.