The invention relates to a feed additive containing a compound amino acid complex as well as a preparation method and application thereof and belongs to the field of feed. The preparation method comprises the following steps: adding a microelement mixed salt solution into compound amino acid solution, so that mixed solution is obtained; cooling until temperature of the mixed solution is not higherthan 20 DEG C, and separating out and drying crystals. The preparation method is simple in technology, easy to operate and convenient for industrialized popularization and application. The feed additive prepared by adopting the preparation method is rich in amino acids and microelements and can relieve weaning stress of a suckling pig and improve skin color and hair conditions of the suckling pig. The feed additive not only can effectively improve a digestion function of the suckling pig and enhance disease resistance of the suckling pig but also can greatly save the usage amount of proteins,reduce feeding cost and improve production efficiency of animals when applied to feed for the suckling pig. Besides, the feed additive provided by the invention also can reduce discharge of fecal nitrogen and urinary nitrogen, effectively improve a pigsty environment and relieve manure treatment pressure.