In this paper, we investigated an easy and fast protein separation and analysis method using the pH composition of buffer solution and sodium dodecyl sulfate (SDS), an anionic surfactant, on microchips. First, to optimize the separation efficiency of microchips, the separation efficiencies at various electric field intensities (238~507 V/cm) were compared using CON protein. The pH of the buffer solution (7~9) was controlled under the same electric field condition, and the separation analysis of the four proteins was performed. As a result, the four proteins were successfully separated at pH 7, an optimal condition. In addition, SDS, an anionic surfactant in a buffer solution, was added to carry out separation analysis of the mixed proteins. As a result, two proteins which had not been separated were selectively bound to SDS in the buffer solution, thereby being successfully separated according to size. This result confirmed that the detection limit of the separation analysis was up to several nM, which was an excellent detection limit. The results of this study are expected to be useful for various studies or applications by enabling identification of protein functions in cell components and development of new drugs.