In the present study, the endocrine toxicity of LCT and PBA was investigated through exposure to Eremias argus for two weeks under environmental relevant concentration. RNA-sequencing identified 4442 and 4653 differentially expressed genes in lizard liver after LCT and PBA exposure. Four differentially expressed genes (hsd17β, ar, sult, ugt) related with hypothalamic-pituitary-gonadal axis were quantified by qPCR. The expression of genes associated with HPG axis in different tissues differed significantly. In LCT treatment group, ar, cyp17 and hsd3β genes involved in testosterone synthesis and transportation were significantly decreased in lizard testes, and the spermatogensis was inhibited in the testes, which indicated the anti-androgenic activity of LCT. After PBA exposure, the genes related with estradiol synthesis, transportation and metabolism, such as hsd17β, erα, ugt in lizard liver were important biomarkers and the significant decrease of estradiol level was highly correlated with hsd17β, erα, ugt gene expressions. The relative high binding affinity of PBA with ERα further demonstrated the anti-estrogenic activity of PBA. Our results elucidate the different toxic mechanism of LCT and PBA on lizard endocrine system at environmental relevant concentration. Pyrethroids metabolism may cause more seriously toxicity rather than detoxification.