This paper presents a novel structured dynamic model to simulate the metabolic reaction network of green algae hydrogen production from aerobic cultivation conditions to anaerobic cultivation conditions, 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. By applying this methodology, the current study constructed an accurate dynamic model whose simulation results are highly comparable to the 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 sulfur concentration in the culture, rather than to modify the activity of specific enzymes.