A transmitted fluorescence detector induced by a Light Emitting Diode(LED) was established for integrating in a microfluidic cell chip.The detector overcomes the problems of system bulky in larger size,higher energy consumption and low coupling efficiency for inducing optical path, detection zone and fluorescence optical path. The angle for induced fluorescence optical path was designed to be 135°. The exciting light produced by the LED passed through an optical lens, an exciting light filter and a diaphragm aperture with a diameter of 200 μm, and then reached the detection zone of microfluidic chip. The induced fluorescence light and stray light passed through emitting high pass interference thin film filter fabricated at the back of the microfluidic chip, and finally was collected by a photomultiplier(PMT). The performance of the fluorescence detection micro system was verified by using HepG2 hepatoma carcinoma cells as samples. The experimental results show when the working current for LED and the control voltage for PMT are respectively set to be 200 mA and 3.5 V, the output is a peak signal which is obviously distinguished from background noise. 8 peak signals with an average value of 0.7 V are obtained within 250 s, which agrees with that from a fluorescence microscope. It shows the detection system realizes the function of cell counting detection, and is a new technological approach to micro total cell analysis systems.