The invention discloses a composite amino-acid-containing water-soluble fertilizer which comprises the following components: amino acid materials, major elements such as N, P and K, secondary elements such as Mg and Ca, minor elements such as Fe, Mn, Zn, B, Mo and Cu, assistants, a pH value regulator and a water solution. The preparation method of the fertilizer comprises the following step: chelating the composite amino acids with six metal elements (Mg, Ca, Fe, Mn, Zn and Cu) at normal temperature (15-(-35) DEG C) according to a specific sequence, thus obtaining the water-soluble fertilizer. According to the composite amino-acid-containing water-soluble fertilizer, 18 amino acids and 11 nutrient elements are enriched, the six metal elements are wholly chelated, all the components are stably dissolved, and no antagonism and precipitation problems exist.