Capillary electrophoresis (CE) is an analytical tool which has gained great interests during the past decade. The main attractions of CE are its fast, high-throughput and highly efficient separations. However, conventional single branch CE system has faced the challenge when samples lack of appropriate internal standards. Thus, a double branch CE configuration is introduced here to solve this problem. We successfully fabricated the two branch microfluidic switch by using standard photolithography and PDMS prototyping. This two-branch switch was placed between the two sample supplies and an injection flow gate. Two samples were alternately injected and then separated by the CE system. The concentration of one sample was maintained constant as the standard while the other contained to-be-determined analyses. This method was able to compensate the effects due to potential drifting of the excitation light source, variation of light focusing, and/or fluctuation of sample injections, which was based on the assumption that the variation of experimental conditions between two successive injections was negligible. The results showed high reproducibility and stability achieved by the two-branch switch. This strategy would be especially valuable at situations when there are no appropriate internal standards for specific analyses.