The fluorescence method is a noninvasive measurement method that can rapidly measure the primary productivity of algae in aquatic systems. However, in the current analysis of fluorescence dynamics of primary productivity, when the photosynthetic size unit of algae is used with a fixed value, the measurement results of the primary productivity of algae in an aquatic system often exhibit deviations, particularly where cyanobacteria existing. The photosynthetic size unit is defined as the ratio of the photosynthetic reaction center concentration to the chlorophyll concentration. Herein, to obtain accurate algae photosynthetic size units and improve the accuracy of the primary productivity, excitation fluorescence spectroscopy was employed to analyze the proportion of cyanobacteria and other eukaryotic algae. As a result, the photosynthetic size unit of the mixed algae sample was corrected, and a fluorescence method based on the photosynthetic size unit correction is proposed to measure the primary productivity of algae. The results of a comparison test of the primary productivity of purebred and mixed samples demonstrate that using the proposed correction method, the measurement errors of the primary production of purebred cyanobacteria, chlorophyta, and pyrrophyta samples are reduced from 38.8%, 14.3%, and 13.2% to 3.9%, 4.1%, and 5.2%, respectively. In addition, the maximum and average measurement errors of the primary productivity of the mixed sample decrease from 20.4% and 15.2% to 4.5% and 5.2%, respectively, compared with those without correction. The proposed method can effectively resolve the measurement result deviation problem caused by the fixed value of the photosynthetic size unit. The proposed method provides an important reference to improve the measurement accuracy of primary productivity of algae in aquatic systems.