The invention relates to a preparing method of water-based self-crosslinked acrylic acid modified polyurethane matte resin. The resin mainly comprises isocyanate tripolymer, polyether polyol or polyester polyol, dimethylolpropionic acid, acrylate, an alkali neutralizing agent and deionized water. The resin prepared by the method is low in VOC content, environmental friendly and free of pollution and is characterized by low-temperature curing performance, a high extinction efficiency, good transparency, protruding water proofness, protruding acid resistance, protruding alkali resistance, protruding stain resistance and protruding yellowing resistance. After modification, polyurethane and hydroxy in acrylic acid resin are crosslinked, thus enhancing the resin crosslinking density, and improving resin mechanical strength, wear resistance and scratch resistance. The matte resin is free of addition of a flatting agent and insensitive to electrolytes. Prepared coating is good in stability. The matte resin is widely used for water-based wood paint, water-based industrial paint, water-based plastic paint, and the like requiring matte effects.