In order to realize the automatic counting of algae, taking chlorella (Chlorella vulgaris) as the target, an automatic counting method based on fluorescence effect and palette equalization was proposed in this paper. Firstly, the fluorescent micrograph of chlorella was pretreated, by transforming it into 256-color images and enhancing its contrast by palette equalization algorithm. Then the target algae and the background were divided using threshold segmentation algorithm of the palette, and simultaneously counted. The results showed that this counting method could avoid the interference of impurities, directly realize the algae color image enhancement and threshold segmentation, increase the image contrast and avoid loss of image information during the process of color image graying; and by using the connected area marking method combined with the size of the connected region to recognize the algae of low overlapping degree, it reduced the influence of overlapping algae on the counting results, and thus could improve the calculation accuracy of chlorella. The experimental results show that this method can achieve automatic counting for algae color images, and the accuracy of chlorella counting accuracy is higher than 95%, which is higher than that of those methods using only gray scale image.