Preparation method and application of astaxanthin H1-, or H2- or J-aggregate water dispersion system are provided. The three kind of color-different astaxanthin multimer nano-dispersion systems utilize a special molecular structure of natural biomacromolecule chitosan and fish sperm DNA as well as physical interaction between macromolecules to induce formation and stability of astaxanthin multimers under solvent and salt ion-effects. Low-toxicity ethanol is selected as a good solvent for astaxanthin. The organic solvent can be completely removed in the later stage of the preparation process, and can be further enriched and recycled, which is beneficial to clean production and low cost. By adjusting process parameters, the H1-, or H2- or J-type astaxanthin aggregate water dispersion system can be obtained, so as to control a coloration range of astaxanthin water-based products to be yellow, orange and pink. Furthermore, during concentration, dehydration and reconstitution, astaxanthin aggregation patterns and coloring effects are maintained.