The present study preliminarily evaluated neurotoxicity injuries induced by chlorpyrifos in PC12 cell, which were used as a model for nervous cell system. In cultured PC12 cell, application of soy isoflavones (genistein, daidzein, monomer and mixture) significantly reduced chlorpyrifos induced toxicity, a widely used pesticide, and resulted in a better cell survival rate. Treatments with isoflavones reduced malondialdehyde content, reactive oxygen-generation and acetylcholine level in medium, and maintained mitochondrial membrane potential integrity. Daidzein enhanced endogenous antioxidant system in PC12 cell with an increasing in superoxide dismutase per-unit activity. Genistein reduced acetylcholine content in the medium. Daidzein and genistein showed different effects, and their combined effect were greater than individual. In conclusion, soy isoflavones as an antioxidant and neuroprotectant, enhanced choline metabolism, which effectively mitigated disadvantageous influence of PC12 cell caused by chlorpyrifos.