The invention relates to a method for comprehensively treating saline alkali soil. The method is characterized in that a method in which physical improvement and biological improvement are combined is used for treatment. According to the physical improvement, project land parcels for treating the saline alkali soil are constructed, a road is constructed in the middle, a ditch is constructed on one side of the road and provided with multiple branches for irrigation of all the land parcels, a salt and alkali discharging branch canal is arranged beside the land parcel on the outermost edge, and the branch canal is converged to a main salt and alkali discharging canal. The biological improvement includes fertilizer preparing, mellow soil insect luring, soil loosening insect killing, planting of any one of saline-alkaline resistant zizania aquatica, corn, astragalus membranaceus, liquorice and chrysanthemum in the next year and crop rotation of crop of the previous year in the third year. Project facility design is scientific and reasonable, operability is high, mechanical operation is convenient, bio-organic fertilizer is applied, soil loosening is convenient through insect luring, saline-alkaline resistant alfalfa planted in the first year returns to the field, the soil is improved, crop rotation is conducted in the second year and the third year, the content of soil salinization of a plough layer is reduced, and meanwhile great economic benefits can be generated from the crop.