The invention discloses a water-based mortar modifier, its preparation method and application. The modifier comprises the following preparation raw materials by mass: 10-20% of polyether polycarboxylic acid water reducing agent, 0.1-10% of air entraining components, 1-20% of coagulation retarding components, 0.1-2% of water retention components and 60-85% of water. The polyether polycarboxylic acid water reducing agent is prepared by the method of: dissolving an enol polyether macromonomer, acrylic acid, and maleic anhydride in water, conducting heating to raise the temperature to 60-70DEG C, then adding a persulfate water solution dropwisely, carrying out heat preservation under 60-65DEG C for 2-4h, then performing cooling to a temperature of 45DEG C, and adjusting the pH value of the system to 7-8, thus obtaining the polyether polycarboxylic acid water reducing agent. The modifier provided in the invention can form a protective film on a cement particle surface, and at the same time can produce uniform and tiny bubbles, as well as reduce the friction between the particles in the system, thus effectively improving the workability and plasticity of the mortar system. Furthermore, the mortar modifier provided in the invention is a water-based multifunctional building mortar modifier, and is convenient to use. Doping of the modifier can significantly improve the workability and vicidity of mortar, and can maintain the properties effectively for 8-16 hours.