The present invention discloses a special compound fertilizer for saline-alkali soil and a production method thereof. The compound fertilizer comprises microbial agents, mineral fertilizers, organic fertilizers, slow-release fertilizers, and controlled-release fertilizers. The microbial agents include halophilic bacteria, alkalophilic bacteria, nitrogen-fixing bacteria, phosphate solubilizing bacteria, potassium bacteria, Bacillus subtilis, Bacillus licheniformis and E. coli; the mineral fertilizers include Chinese medical stone, calcite and zeolite; the organic fertilizers include one or more of cow manure, horse manure, chicken manure, humic acid, milk vetch, alfalfa, crushed straw, leaf mold, soybean meal, peanut meal, fermentation product residues; the slow-release fertilizers include calcium superphosphate and urea formaldehyde; and the controlled-release fertilizers include ammonium sulfate, potassium chloride, potassium sulfate and ammonium chloride coated by semi-permeable membranes with different thicknesses. The fertilizer can effectively improve soil structure, reduce salinity and pH value of the soil, increase soil fertility, and maintain lasting fertility, and is particularly conducive to improving the saline soil.