We demonstrate a membrane-based microfluidic in vitro cultivation system that regulates the pattern of mechanical stimulation using a micro-modulated syringe pump. Using independent control of flow and compressive force, we applied an in vivo-like mechanical stimulus to bovine embryos in a microfluidic channel. To compare the accuracy of the compressive strain, we observed any morphological change in the embryos using a lateral view of the microfluidic device. Moreover, the compressive strain via mechanical stimuli with different duration times was analyzed. Based on the mechanical behavior of the stimulated embryos, we found that both the amplitude of the pressure and the duration of the stimulus were significant factors. The device is expected to be useful for the development of new methods to precisely control the mechanical stimulation of embryonic growth by mimicking peristaltic constriction in vivo.