The dataset was constructed from the results of mouse experiments. The files with prefix ‘chapter 2’ were the data of embryo development, blastocyst attachment assay and implantation site number after blastocyst transfer. The files with prefix ‘chapter 3’ were the data record of mouse body weight, litter size, pregnancy outcomes, estrus cycle and steroid hormone level of female mice after chronical low-dose bisphenol exposure. This dataset also includes the results files of ovary follicle counting, IHC staining assay and TUNEL assay.