Abstract: Using the second law of thermodynamics the exergy photosynthetic biological hydrogen production system was analyzed by a white-box model.The results show that the yield of hydrogen was less and the exergy efficiencies of the system is 24.4%, and light losing is the biggest one in the total exergy losing which account for 64.4%. Factors that affect the light conversion efficiency was analyzed in the weak links of the system and the corresponding solutions were proposed. The aspects in system and the utilization of the effective energy were improved and a science reference for the process of the industrialization in the photosynthetic biological hydrogen production system were provided.