The invention discloses cement-based polymer mortar specially used for repairing and a preparation method of the mortar, and relates to the technical field of building mortar. The mortar comprises thefollowing raw materials: Wudalianchi volcanic mud, modified composite mineral micropowder, phosphogypsum residues, sodium-based bentonite, diabase fibers, aminopropyltriethoxysilane, a silicone resinpolyether emulsion, sodium tripolyphosphate, polyacrylamide, calcium chloride, an adhesion auxiliary agent, a water reducing agent, a foaming agent and an anti-irradiation agent; and the mortar is prepared by performing mixing and grinding on the raw materials. The mortar disclosed by the invention is simple and convenient for preparation, and has the characteristics of excellent workability, volume structure stability, high compressive bonding strength, shock resistance, cracking resistance, seepage resistance, freeze resistance, corrosion resistance and the like; and the mortar has remarkably improved application durability, long service life and a wide range of application.