Progestins and estrogens are widespread in various aquatic environments and their potential endocrine disruption effects to aquatic organisms have drawn growing concern. However, their combined effects in aquatic organisms remain elusive. The aim of the present study was to assess the effects of the binary mixtures of gestodene (GES) and 17α-ethinylestradiol (EE2) on the hypothalamic–pituitary–thyroid (HPT) axis of zebrafish (Danio rerio) using the eleuthero-embryos. Embryos were exposed to GES and EE2 alone or in combination at concentrations ranging from 41 to 5329 ng L−1 (nominal ones from 50 to 5000 ng L−1) for 48 h, 96 h and 144 h post fertilization (hpf). The results showed that the transcripts of the genes along the HPT axis displayed pronounced alterations. There was no clear pattern in the change of the transcripts of these genes over time and with concentrations. However, in general, the transcripts of the genes were inversely affected by EE2 (increase 0.5 to 4.2-folds) and GES (inhibition 0.4 to 4.9-folds), and their mixtures showed interactive effects in embryonic zebrafish. In addition, physiological data (mortality, malformation, body length and heart rate etc.) denoted higher toxicity of the two chemicals in combination than alone based on the developmental toxicity and neurotoxicity (locomotor behavior). These results indicated that the interactive effects of these two chemicals might be different between at the transcriptional level and at the whole organismal level. In summary, GES and EE2 affect the HPT axis (related genes expression and thyroid hormones (THs) levels) and exhibit developmental toxicity and neurotoxicity.