The invention discloses a preparation method of a compound amino acid injection containing peptides. The preparation method comprises following steps: under nitrogen protection, injection water with a total volume dose less than 90% is boiled; the boiled injection water is cooled to 80 to 100 DEG C, amino acids are added at formula dosages, and then the boiled injection water is cooled to 65 to 85 DEG C, and amino acids are added at formula dosages, wherein the amino acids added in the step are different amino acids; the boiled injection water is cooled to 55 to 75 DEG C, and glycyl-L-glutamine, glycyl-L-tyrosine, and arginine are added at formula dosages, an obtained mixture is stirred and clarified, and alanine, histidine, proline, and serine are added at formula dosages; an obtained mixed material is cooled to 40 to 55 DEG C, tryptophan is added at a formula dosage, a compound amino acid aqueous solution is obtained via uniform stirring, and pH value is adjusted to 5.0 to 6.5 with a pH conditioning agent. According to the preparation method, dissolving of different amino acids is realized gradually in different temperature ranges, so that amino acid solubility is increased, and stability is not destroyed.