The invention relates to a microorganism immobilization method. The method comprising the following steps of: taking a sodium alginate solution containing dense suspending microorganisms and nano calcium carbonate as disperse phases, taking atoleine or vegetable oil as a disperse medium, and taking Span85 as a surfactant; forming droplets through agitation and emulsification; then preparing calcium alginate bead gel embedding the microorganisms through a gel initiator of glacial acetic acid; forming a polycation-polysnion complexing membrane through the reaction and cross linking of the bead gel and a chitosan solution; and finally forming a sodium alginate-chitosan microcapsule embedding the microorganisms. The method has mild conditions in the preparation process, simple requirements on apparatuses and equipment, easy mass production, good maintenance of the activity of the microorganism cells in the preparation process, and lower cell leakage rate. Thus, the technology is suitable for the immobilization embedding of a plurality of microorganisms such as yeast, bacillus coli, lactic acid bacteria, nitrobacteria, etc., thereby realizing high-density and large-scale microorganism culture.