The paper aims to propose an adaptive brightness correction and low contrast enhancement algorithm for fluorescence images to improve the background illumination unevenness and low contrast of fluorescent images. According to the principle of illumination imaging, the illumination component of the fluorescence image was extracted by guided filtering. The background illumination was dynamically corrected by the improved two-dimensional Gamma function. The corrected foreground and background were separated by Top-hat transformation. And the adaptive histogram equalization was performed on the foreground, to have adaptive enhancement of fluorescent images. Compared with the traditional algorithm, the background illumination of the image processed by the algorithm was uniform and the contrast enhancement effect was obvious. The standard deviation was improved by 9.4 times; the average gradient was increased by 1.2 times; and the information entropy was increased by 0.2 times. The algorithm can improve the background illumination unevenness of high-throughput dPCR fluorescence image, improve the image contrast, highlight hidden details in the image, and has reference value for processing of other fluorescence images.