The invention provides formula goat milk powder with abundant omega-3 polyunsaturated fatty acids and a preparation method thereof. The goat milk powder is prepared from, by weight, 400-700 parts of raw goat milk/full-cream goat milk powder, 100-200 parts of skimmed milk powder, 80-100 parts of Isomaltooligosaccharide, 50-100 parts of 55% fructo-oligose, 50-150 parts of D90 demineralized whey powder, 50-100 parts of soybean oil, 20-60 parts of WPC34 whey albumen powder, 10-20 parts of linseed oil, 5-10 parts of lecithin, 1-5 parts of deep sea fish oil DHA, 1-5 parts of deep sea dish oil EPA and 0.5-1 part of bifidobacterium lactis/lactobacillus casei; the preparation method comprises the following steps of premixing, high pressure homogenizing, first-time sterilization, concentration, second-time sterilization, high pressure spraying, drying and dry mixing. The advantages and functions of the omega-3 polyunsaturated fatty acids, probiotics and goat milk powder are synthesized, the nutrient formula goat milk powder has the better functions, the component ratio is reasonable, the human brain development is promoted, the human body ingewanden functions are improved, vision developmentis promoted, the immunity is enhanced, and high nerves are comprehensively nursed.