Rapid and accurate assessment of the primary productivity of phytoplankton is crucial to scientific research of marine ecological environment and understanding of evolution rules of global carbon cycle. The measurement period of primary productive forces represented by the 14C tracer method or the black and white bottle method is long and cumbersome. To solve the problem, we study the photosynthetic electron transfer rate according to the biofilm energy flow theory. Photosynthetic parameters are obtained by the variable chlorophyll fluorescence induced by light source, and combined with photosynthetic electron transfer rate “biological-optics”. Therefore, the measurement of photosynthetic electron transfer rate based on fluorescence kinetic parameters is studied. The chlorella pyrenoidosa is tested under different stress conditions, and the photosynthetic oxygen rate measured by the liquid phase oxygen electrode is compared to verify effectiveness of the photosynthetic electron transfer rate. The results show that under different concentrations of dichlorophenyl dimethylurea stress, the photosynthetic electron transport rate and photosynthetic oxygen release rate of phytoplankton have good consistency, and both decrease significantly with the increase of the stress concentration. The photosynthetic oxygen release rate and photosynthetic electron transport rate are reduced by 71.55% and 68.87%, respectively, and their square of correlation coefficient is 0.934. Under different nutrients or light intensity for 15 d, the photosynthetic electron transport rate and photosynthetic oxygen release rate still have good consistency, and their square of correlation coefficient is greater than 0.955.