In this paper, the feasibility of immobilization of sodium alginate gel for the treatment of fermentation raffinate from biohydrogen production was studied. Five fermentation raffinates, which were produced from alfalfa dark fermentation biohydrogen production, photo-fermentative biohydrogen production from mixture of cow dung and corn straw, photo-fermentative biohydrogen production from corn stover and corncob, and dark fermentation biohydrogen production from corn stover, were utilized as raw materials, to prepare the gel microspheres. Two immobilization methods of positive titration and reverse titration were evaluated. Mass concentration of 3% sodium alginate solution and 10% CaCl2 solution were adopted as embedding medium, results showed that the fermentation raffinate could be gel fixed by sodium alginate immobilization method. In order to get the best immobilization conditions, the effects of different concentrations of CaCl2 and sodium alginate on the immobilization were analyzed by single factor experiment. Fixed sodium alginate concentration at 3%, and different CaCl2 concentrations of 1%, 2%, 4%, 6%, 8%, 10% were set for gel fixation. The results showed that 2% CaCl2 fixation effect was the best. Then, fix the mass concentration of CaCl2 at 2%, and different sodium alginate concentrations were set at 1%, 2%, 3% for gel fixation. The results showed that 2% concentration of sodium alginate has the best fixation effect. It can be concluded that 2% sodium alginate solution and 2%CaCl2 solution have the best effect on the immobilization of fermentation raffinate from biohydrogen production. Nitrogen, phosphorus, potassium and other elements in the fermentation raffinate can be slowly released from the fixed gel microspheres. The results of hydroponic experiments showed that all the five kinds of hydroponic microspheres could provide nutrition for the germination and growth of black leaf cabbage seeds.