The invention relates to malic acid phosphate ester and applications of the malic acid phosphate ester in inhibition of calcium ion deposition diseases, wherein the structure of the malic acid phosphate ester is represented by the following formula. The synthesis steps comprise: carrying out a stirring reaction of malic acid and benzyl alcohol for 6 h at a temperature of 80-130 DEG C, carrying out pressure reducing distillation at a temperature of 175-185 DEG C to remove the unreacted benzyl alcohol, carrying out recrystallization with ethanol to obtain dibenzyl malate, dissolving the dibenzyl malate in dichloromethane under N2 protection, adding triethylamine, adopting 4-dimethylaminopyridine as a catalyst, stirring for 0.5 h in a 0 DEG C ice bath, slowly adding diphenyl chlorophosphate in a dropwise manner, carrying out a stirring reaction for 0.5 h, carrying out a room temperature for 12 h, carrying out pressure reducing distillation, carrying out recrystallization with ethanol to obtain dibenzyl phosphate ester dibenzyl malate, adding the dibenzyl phosphate ester dibenzyl malate and platinum oxide to distilled water, carrying out a catalysis reaction for 20-24 h, extracting, and carrying out low temperature freeze-drying to obtain the product. According to the present invention, with the malic acid phosphate ester, the mouse myoblast C2C12 calcification can be well inhibited, and the concentration of the calcium ions in the human skeletal muscle cell HSK can be effectively reduced.