The invention relates to a process for treating free alkali in red mud by microorganisms. The process comprises the steps of: injecting red mud in a stirring tank in percentage by weight after size mixing; adding an acid solution containing domesticated lactic acid bacteria or thiobacillus ferroxidans, controlling the temperature, pressure and a pH value, filtering ore pulp after being treated by microorganisms to obtain a microorganism-containing solution and red mud after being treated by the microorganisms, and sending filtrate to a microorganism culture tank for continuing culturing the microorganisms, wherein the free alkali in the red mud is less than 0.95 percent, and reaches the requirement of land rehabilitation. The process has the beneficial effects that the acid used by the process is microorganism organic macromolecule weak acid, thus compared with a treatment method using inorganic acid or alkali in the prior art, the process has the advantages of reducing cost, being high in rate of removing the free alkali, short in period, simple in process, low in cost, few in impurities in leachate, low in equipment corrosion rate, convenient for storage and transportation, and beneficial to culture and recycling of microorganisms in a subsequent solution; the treated red mud filter cake contains less than 0.95 percent of free alkali, the environmental harm to the soil is reduced, and the land rehabilitation and utilization can be performed.