According to the biological film energy flow theory and electron transfer model, the plant complex photosynthesis is analyzed and simplified by combining to the exciting conditions of fast phase and relaxation, so that an inversion method of plant photosynthesis parameter is proposed .The maximum fluorescence yield is calculated by using the determinate method of sliding window slope. The photochemical quantum efficiency and the functional absorption cross section are obtained by analyzing the fast phase fluorescence process with linear least square algorithm. The plastoquinone average reduction time constant is obtained by analyzing the relaxation fluorescence process with discrete iterative algorithm. The experimental measurement results of the merismopedia and scenedesmu sobliquus grew in logarithmic phase and under the copper ion stress conditions show that the inversion has good stability and repeatability. The relative standard deviation of the photochemical quantum efficiency, the functional absorption cross section and the plastoquinone average reduction time constant are 1.25%, 1.50% and 1.83%, respectively. The linear correlation coefficient of the photochemical efficiency compared to the measuring result of the pulse amplitude modulation technology is 0.9714. The proposed inversion method provides an optical analysis means for the study of plant physiology.