The invention discloses environment-friendly water-based ink, and an an environment-friendly high-strength compression-resistant color box and a manufacturing method thereof. The environment-friendlywater-based ink is prepared from the following raw materials in parts by weight: 25-35 parts of epoxy acrylic resin, 10-15 parts of fluorosilicone modified acrylate emulsion, 5-8 parts of hydroxy cellulose, 10-30 parts of colorant, 5-20 parts of nano calcium carbonate, 1-3 parts of cerium dioxide, 0-11 parts of butyl cellosolve, 5-10 parts of triethanolamine, 0.5-0.8 part of defoamer, 0.5-1.0 partof sodium hexametaphosphate, 0.5-1.1 parts of trimethoprim, 0.5-1.5 parts of an auxiliary agent, 15-25 parts of deionized water and 3-5 parts of isopropanol. According to the invention, the corrugated paper of the middle layer of the color box is folded into a corrugated structure, so that the stability of the structure of the middle layer is improved, and the situation that the corrugated paperis impacted and deformed, and consequently the corrugated structure in the corrugated paper is damaged is reduced.