The invention relates to a special-effect health indoor wall aqueous paint composition and a preparation method thereof, and belongs to the field of aqueous paint compositions for construction decoration. The paint composition is composed of the following raw materials in parts by weight: 20 to 30 parts of water, 0.2 to 0.5 part of thickening agent, 0.05 to 0.2 part of pH adjuster, 0.1 to 0.3 part of antifoaming agent, 0.1 to 0.4 part of wetting agent, 0.2 to 0.7 part of dispersant, 10 to 25 parts of nano titanium dioxide, 1 to 10 parts of nano diatom ooze, 2 to 10 parts of embedded anionic nano silicon dioxide, 20 to 40 parts of filling material, 9 to 18 parts of emulsion, 0.2 to 0.7 part of anti-freezing agent, 0.1 to 0.5 part of film-forming auxiliary agent, and 0.2 to 0.4 part of bactericidal mildew inhibitor. The paint composition can absorb the harmful components in air, is healthy and environment-friendly, and also has the advantages of excellent color retention, scrubbing resistance, water and alkali resistance, and proper softness of paint film.