Xenopus is as an important and efficient animal model to study various diseases, because it readily manipulates the large numbers of embryos as well protein expression. Morphological evaluation of massing Xenopus at different stages is an essential procedure, but it currently requires labor-intensive and manual inspection under optical microscope. Here, we propose the high-throughput monitoring method via customized imaging tool and customized PDMS microwell plate. We also developed the home–built analysis software to accelerate the value of our device.