The invention discloses a special saline-alkali-soil improvement fertilizer prepared by modification with flue gas desulfurization gypsum and a preparation method thereof. The special improvement fertilizer comprises the following components in parts by weight: 40-80 parts of flue gas desulfurization gypsum, 1-3 parts of citric acid, 0.5-1.5 parts of magnesium sulfate, 1-5 parts of aluminum sulfate, 1-5 parts of ferrous sulfate, 10-30 parts of weathered coal, 10-20 parts of cattle manure or chicken manure, 1-5 parts of urea, 0.5-2.5 parts of ammonium sulfate, 1-3 parts of potassium sulfate, 1-3 parts of monoammonium phosphate, 0.1-0.5 part of zinc sulfate, 0.1-0.5 part of manganese sulfate and 3-10 parts of bentonite. The fertilizer is reasonable in design, provides an effective solution for inland saline-alkali soil of China, and has higher practical value and wide market prospects.