A cross-polarization scheme and vertical multi-layer structure is presented to filter out the excitation light from the emission spectrum of fluorescent dyes using green organic light emitting diode as light source and a linear charge coupled device as intensity detector. Micro lens array film was affixed on glass base of organic light emitting diode in order to improve the incident intensity. Electrophoretic separation were performed with Rhodamine B as sample solution under the optimal parameters including integral time of CCD, diameter of PDMS micro lens and two polarizers’ polarization angle in the detection system.