Abstract: Separation of two colored model proteins, cytochrome C and hemoglobin, were conducted in the specially self-designed free flow electrophoresis device A3-2 using zone electrophoresis mode under 1 g- and μg- conditions. The results demonstrated that the higher resolution of free flow electrophoresis acquired under the microgravity is obtained. Both onboard LBD detection and measurement of the seperation by the spectrometer demonstrated that the distance between the zone maxima of the two proteins were increased and the dispersion of hemoglobin decreased. The experiments also included: （1） The effect of the glycerol concentration on the separation results; （2） Post-flight analysis of the contents of the fractions. The separation results of 10%, 7%, 4%, 2% and 0% glycerol concentration in the electrophoresis buffer are compared and no significant effect of the glycerol on the separation results are found. So the glycerol and its disadvantages for the clean and storage of the device were excluded finally. Gel electrophoresis and mass spectrometry analysis of the contents of the fractions confirmed that two proteins have been effectively separated.