The invention provides a soft soil shield tunnel lining segment behind microorganism grouting method which is mainly used for a soft soil shield tunnel. In secondary grouting through the tunnel, prepared and cultured nutrient solution and denitrification bacteria capable of generating nitrogen and carbon dioxide gas are injected into a slurry outer soil layer together through a designed grouting device, the denitrification bacteria can breed and grow and generate the nitrogen and the carbon dioxide gas in the process, the nitrogen can replace water in the soil layer to form a bubble layer, penetrability of the soil layer is reduced, an appropriate amount of carbon dioxide gas and a slurry layer are subjected to carbonization reaction, slurry gaps are filled with calcium carbonate serving as a reaction product to a certain degree, and the strength and penetration resistance of slurry are enhanced. Double-layer active defense barriers for pollution and erosion water are formed, so that penetration of pollutants and saline solution to a tunnel structure is reduced, and active corrosion resistance and erosion resistance of the tunnel structure are improved.