This paper presents a novel structured dynamic model to simulate the metabolic reaction network of green algae hydrogen production from aerobic condition to anaerobic condition, which has not been addressed in the open literature to this date. An efficient parameter estimation methodology is proposed to avoid the difficulty of measuring essential kinetic parameters from experiments. The accuracy of the model is verified by comparison to published experimental results. The current model finds that the starch generation pathway mainly competes with hydrogen production pathway, as its activity is enhanced by the cyclic electron flow pathway. From the dynamic sensitivity analysis, it is concluded that the most effective solution to enhance hydrogen production is to seek the optimal sulphur concentration in the culture, rather than to modify the activity of specific enzymes. The current work also denies the previous hypothesis that the diffusion of small proteins in the metabolic network inhibits hydrogen production.