Zhuyun recipe (ZYR) is a traditional Chinese medicine that has been widely used as an infertility treatment for a number of years. Although the therapeutic effects are desirable and satisfactory, the therapeutic mechanism of ZYR remains poorly understood. In the present study, pinopodes were investigated as an important morphological marker of endometrial receptivity, in order to further investigate the therapeutic mechanism of ZYR. The expression of pinopodes during the implantation window was observed using scanning electron microscopy in mice with induced ovarian stimulation (OS) and embryo implantation dysfunction (EID). A marked decrease in the number of fully developed pinopodes was observed on the endometrial surface in the OS and BID model mice, which was in accordance with the decreased pregnancy rate and number of embryonic implantation sites when compared with the control. Following treatment with ZYR, the spatial and temporal expression of pinopodes in the OS and EID mice was found to be similar to the control mice. In conclusion, ZYR was demonstrated to improve endometrial receptivity in OS and BID mice through significant improvements in the spatial and temporal expression of pinopodes.