Haematococcus pluvialis is a good source of astaxanthin, which reduces oxidation in the human body, treats inflammation, and slows the growth of breast and skin cancer cells. Since the size of H. pluvialis is often closely related to astaxanthin yield, size-based microalgal separation has far-reaching significance for high-value algae extraction and algal directed evolution. In this work, we report a novel size-tunable elasto-inertial sorting of H. pluvialis in the Ecoflex ultrastretchable microfluidic devices. Ecoflex microfluidic chips can deform and be flexible, bringing flexibility and stretchability to microchannels as well as new possibilities for large-scale modulation of channel geometry. Here, the effects of velocity, channel elongation, and particle size on the elasto-inertial migration of particles are systematically studied. We found that channel elongation has a strong regulating effect on particle focusing. In addition, we verified the continuous regulation of the sorting threshold of microalgal cells by stretching the channel, providing technical support for the extraction and directed evolution of high-yield microalgae.