The invention relates to a magnesium phosphate cement based rapid repair mortar and a preparation method thereof. The rapid repair mortar includes the following components by weight: 100 parts of magnesium phosphate cement, 6-50 parts of a mineral admixture, 50-300 parts of fine aggregate, and 10-30 parts of water. The magnesium phosphate cement is obtained by mixing of, by weight, 60-70 parts of metal oxide powder, 20-28 parts of phosphate, 3-6 parts of a retarder and 4-6 parts of a coagulation regulating component. The magnesium phosphate cement based rapid repair mortar is prepared by adopting magnesium phosphate cement as the cementing material, adopting dipotassium phosphate for coagulation regulating modification, and using sand as the fine aggregate, then adding a proper amount of mineral admixture, and performing mixing with water. Compared with the prior art, the magnesium phosphate cement based rapid repair mortar provided by the invention has the advantages of controllable coagulation time, high bonding strength, good stability and high water resistance, etc.