Light emitting diode (LED) can be used in the treatment of jaundice. Blue and green LED irradiation affected with the newborn is currently considered the most effective treatment of the jaundice in the world. A jaundice phototherapy system with blue and green LED as light source utilizing fly eye lens array was built to achieve uniform illumination in the present study. AMC7150 chip was used to build the constant current drive module, and AT89C52 MCU and LCD12864 LCD screen were used to build the human-computer interaction module. Based on national particular phototherapy equipment requirements (YY0669-2008) for the safety, we designed and implemented a phototherapy system which spot area was 250 mm×500 mm, blue light irradiance reached 2 mW/cm2, green light irradiance reached 1.5 mW/cm2, and the uniformity of light was over 90%. Compared with the traditional system, the new one designed in this study has better therapeutic effect, higher biological safety, easier to achieve man-machine interaction, and more economical and convenient.