The invention discloses a preparation method of novel biological matrix non-soap type core-shell structure water-based acrylic acid emulsion. The preparation method comprises the following steps: 1) adding fatty acid, monobasic acid and polyol with natural source according to a certain proportion to prepare an alcohol acid intermediate; 2) adding a certain amount of polybasic acid and anhydride into the alcohol acid intermediate prepared in the step 1 according to a certain proportion and dissolving into water to prepare an alcohol acid aqueous solution; and 3) adding an acrylic acid comonomerin the alcohol acid aqueous solution in the step 2 at a time or in batches, adding an initiator, a reducing agent, a catalyst, a molecular weight regulator, reacting at 30 to 95 DEG C for 10 to 90 minutes, adding aids such as a crosslinking agent, a sterilizing agent, preservative, a stabilizer and a defoaming agent as required, and finally obtaining the novel biological matrix non-soap type core-shell structure water-based acrylic acid emulsion. The emulsion has the advantages of environmental friendliness, reproducible raw materials, low cost, high drying speed, wide and adjustable film-forming temperature and hardness and the like, and is favorable for application and popularization of biological matrix concept products.