Microalgae separation technology is essential for both executing laboratory-based fundamental studies and ensuring the quality of the final algal products. However, the conventional microalgae separation technology of micropipetting requires highly skilled operators and several months of repeated separation to obtain a microalgal single strain. This study therefore aimed at utilizing microfluidic cell sorting technology for the simple and effective separation of microalgae. Microalgae are characterized by their various morphologies with a wide range of sizes. In this study, a contraction-expansion array microchannel, which utilizes these unique properties of microalgae, was specifically employed for the size-based separation of microalgae. At Reynolds number of 9, two model algal cells, Chlorella vulgaris (C. vulgaris) and Haematococcus pluvialis (H. pluvialis), were successfully separated without showing any sign of cell damage, yielding a purity of 97.9% for C. vulgaris and 94.9% for H. pluvialis. The result supported that the inertia-based separation technology could be a powerful alternative to the labor-intensive and time-consuming conventional microalgae separation technologies.