The human papilloma virus (HPV) gene chip detection device can read and analyze the hybrid point signal values of the HPV chip to distinguish different HPV virus types. The uniform illumination of the device is related to the difficulty and reliability of the HPV chip image processing algorithm. To achieve uniform illumination, the rectangular LED array is arranged and the uniform light diffusing plate is arranged. Firstly, the radiation intensity distribution of a single LED lamp bead is analyzed to establish a theoretical model of the rectangular LED array. Then, a rectangular LED array model of 4 rows and 8 columns is established in the simulation software. Finally, the HPV gene chip detection device is set up for experimental testing. The experimental results show that the illumination system has a gray level uniformity of 95.6% in the target surface of 70 mm×20 mm, which meets the uniform illumination requirements of the HPV gene chip detection device.