A micro-free flow electrophoresis (μFFE) analytical system with voltage applied in two dimensions was proposed. Both fluid transport and separation were driven electrokinetically. The Alpha-Imager was applied as an in-situ detector, which could observe, scan and analyze the photometric state of the whole separating area. The mass-transfer process and the range of voltages applied on the chip were simulated and calculated by MATLAB software. Then, the chip design with a separating chamber, which was 12 mm in length, 5 mm in width and 20 μm in depth, was presented. Under the CZE-CZE mode, the operational conditions, such as the EOF, the pH of the buffer and the ratio of the voltage applied in two dimensions, were optimized. Mixed amino acids, including FITC-labeled L-lysine, FITC-labeled L-phenylalanine and FITC-labeled L-aspartic, were successfully separated on the chip when the borate buffer contained 3% glycerol, with pH as 11 and the ratio of field strength in two-dimension was 1:7. The resolution could achieve 2.1 and 1.9, respectively.