The invention discloses a compound aquatic microcapsule initial baits, a preparation and application of the initial baits. The initial baits are prepared by mixing the following main materials mixed in different proportion: maggot protein polypeptide, edible fungus fermentation liquid, lactobacillus, spirulina powder, soya lecithin and vegetable oil with sodium alga acid according to proportion, carrying out high-speed homogenizing, pressurizing, and spraying the mixture into CaCl2 liquid form micro capsules, and filtrating. The diameters of the initial baits are from micrometers to millimeters and the initial baits can suspend in water in a certain time. The initial baits are suitable for newly hatched aquatic seedlings in different growth stages, can strengthen body immunity, regulate ecological balance of intestinal and promote the growth and development. The initial baits meet the requirements on Green feed and feed addictives due to no antibiotics and shell element and no chemical residue, also have the advantages of low cost, convenience in usage and can be widely adopted in aquatic breeding and aquaculture fields.