The invention relates to a method for preparing a composition of peptide, calcium and magnesium, which mainly comprises the following steps: adding collagen peptide into soluble calcium and magnesium to supplement the peptide, calcium and magnesium lost from human bodies, heating an eggshell to change the eggshell into active calcium which is then dispersed in water, adding bittern and liquid sodium hydroxide into the dispersion to generate precipitates of calcium hydroxide and magnesium hydroxide, dehydrating and drying the precipitates to form a dry calcium magnesium hydroxide solid, dispersing the solid in water, adding acetum into the water to form solution of water-soluble calcium magnesium acetate in addition, adding an enzyme into fish scales to hydrolyze the fish scales to form solution of peptide, adding the solution of calcium magnesium acetate into the solution of peptide, after heating to sterilize the mixture, filtering the mixture to obtain the solution of peptide, calcium and magnesium, and concentrating and drying the solution of peptide, calcium and magnesium to obtain the composition of the peptide, the calcium and the magnesium. The composition of the peptide, the calcium and the magnesium has obvious prevention and treatment effect on human bodies, improves the intake rate of the calcium through the antagonism of the calcium and the magnesium, prevents the excess calcium from entering cells to generate side effect, can safely and simply absorb a proper amount of the calcium, and is more practical and convenient in the comprehensive application and use.