Upgrading bioreactor under solar radiant heating can maintain the anaerobic fermentation process by utilizing absorption and scattering of solar energy in media to improve slurry temperature. Finding the suitable correction factor of temperature fluctuation for calculating kinetic rate of microbial fermentation process can improve simulation accuracy of microbial fermentation process. In present work, a coupled model for simulating the processes of photothermal transmission and anaerobic fermentation was built. Experimental and numerical researches about the anaerobic fermentation process of upgrading bioreactor were made to investigate the effect of temperature fluctuation on the kinetic rate of biochemical reactions. The results show that the temperature fluctuation has big effects on the biochemical reaction rate of each substance in the fermentation process. The n values for calculating heat exchange number BT are discrepant for both different reactants and temperature differences. For instance, when the temperature difference is bigger than 4 K, n = 2 is suitable to the one of cow dung in reactor A, and n = 3 is suitable to the one of pig dung and straw pitch in reactor B. The effect of n values on daily biogas production of straw is bigger than the one of cow dung, since hydrolytic bacteria are more sensitive to temperature fluctuation.