Cypermethrin (CP) is a kind of chiral pesticides that has been defined as endocrine disrupting chemical. The diversity in bioactivity, toxicity, metabolism, bioaccumulation, and degradation behaviors of CP enantiomers as well as the research deficiency had made the risk assessment of CP enantiomers very complicated. Herein, four CP enantiomers were separated as target chemicals to investigate their enantioselective endocrine disrupting effects. Firstly, dual-luciferase reporter gene assays were adopted to investigate their potential endocrine disrupting effects via various receptors. The expression levels of steroid hormones related genes and hormone secretion levels in H295R cell were measured to verify the results. Results from the reporter gene assay showed that 1R-cis-αS-CP (CP11) exhibited glucocorticoid receptor (GR), mineralocorticoid receptor (MR), and thyroid receptor (TR) antagonistic activity with the RIC20 values of 9.22 × 10−7, 3.33 × 10−7, and 4.47 × 10−7 M, respectively; 1R-trans-αS-CP (CP21) also showed androgen receptor (AR) agonist activity and estrogen receptor (ER) antagonistic activity with the REC20 and RIC20 values were 1.07 × 10−4 M and 4.78 × 10−6 M, respectively. Results of qRT-PCR and hormone measurement also showed that CP11 and CP21 could disturb the expression of steroid hormones related genes and hormone secretion accordingly. Results provided here can help to understand the enantioselective ecological and health risks of CP enantiomers comprehensively and provide constructive guidance for the safe use of chiral pesticides and the invention of green pesticides.