A simply fabricated microfluidic device using a green organic light emitting diode (OLED) and thin film interference filter as integrated excitation source is presented and applied to fluorescence detection of proteins. A layer-by-layer compact system consisting of glass/PDMS microchip, pinhole, excitation filter and OLED is designed and equipped with a coaxial optical fiber and for fluorescence detection a 300 microm thick excitation filter is employed for eliminating nearly 80% of the unwanted light emitted by OLEDs which has overlaped with the fluorescence spectrum of the dyes. The distance between OLED illuminant and microchannels is limited to approximately 1 mm for sensitive detection. The achieved fluorescence signal of 300 microM Rhodamine 6G is about 13 times as high as that without the excitation filter and 3.5 times the result of a perpendicular detection structure. This system has been used for fluorescence detection of Rhodamine 6G, Alexa 532 and BSA conjugates in 4% linear polyacrymide (LPA) buffer (in 1 x TBE, pH 8.3) and 1.4 fmol and 35 fmol mass detection limits at 0.7 nl injection volume for Alexa and Rhodamine dye have been obtained, respectively.