A dissipative rate model is established by using the non-equilibrium thermodynamics method to evaluate photosynthetic bio-hydrogen production process. The mass transfer dissipation rate, chemical reaction dissipation rate and total dissipation rate for the bio-hydrogen production processes with glucose and acetic acid are calculated and analyzed respectively by using the proposed dissipation rate model. When substrate concentration is taken as variable (15 g/L,20 g/L and25 g/L), the total dissipation rate and mass transfer phenomenological coefficient of hydrogen production process with 20 g/L are the lowest, and the maximum dissipation rate is 7.7288J/h. The phenomenological coefficient of chemical reaction is larger at high concentration. When the temperature is variable (298.15 K,303.15Kand308.15 K), the dissipation rate is lowest at 303.15 K and the chemical reaction coefficient is largest and the maximum dissipation rate is 6.0596J/h. In addition, the mass transfer phenomenological coefficient is larger at high temperature. With the initial pH as variable (6.5,7.0,7.5), the maximum dissipation rate of 11.2271J/h is obtained at pH 7.5. At high pH, the mass transfer phenomenological coefficient is large and the chemical reaction coefficient is exactly the opposite. This model can predict the energy dissipation law in the process of photosynthetic biohydrogen production, and provide a theoretical basis for the subsequent process optimization.