The invention provides a preparation method of a color-changeable natural pigment water-based manicure agent, which comprises the following steps: (1) washing carmine radish, cutting into particles, soaking with absolute ethyl alcohol, filtering, soaking residues again, and combining filtrate; (2) performing vacuum concentration on the filtrate; (3) purifying the concentrated solution to obtain an eluent; (4) carrying out vacuum concentration on the eluent, and freeze-drying to obtain carmine radish pigment; (5) adding pectin into the calcium chloride solution, and stirring to obtain colloidal liquid; (6) adding the carmine radish pigment into the colloidal liquid, and stirring to obtain liquid A; (7) uniformly mixing water-based acrylic resin and polyacrylic resin, and adding the mixture into the liquid A to obtain liquid B; and (8) adding neutral aluminum oxide into the liquid B, and stirring. According to the color-changeable natural pigment water-based manicure agent, the high-purity carmine radish pigment is adopted as the coloring agent, and the coloring agent is a natural pigment, is free of toxic and side effects, is good in safety and can present different colors under different pH conditions.